When the chaos of the election process became clear, many Scots felt humiliated. "The world will be laughing at us". Three guddles had added up to a terminal fankle. Firstly, postal votes went undelivered by the thousand. Secondly, the new computers hired to replace manual counting and give a faster result broke down all over Scotland. Many declarations were delayed by up to twelve hours as returning officers sent their exhausted staff home for the night. But thirdly, and gravest of all, the voters failed to cope with the revised ballot-papers, redesigned from their familiar form because the governing Labour Party felt that the old lay-out discriminated against their own candidates.

The Scottish parliamentary elections use the "additional member" method (AMS), well-tried in many countries. It offers two votes: a cross against the name of a local constituency candidate and a second one for a regional party list. But on top of that, the 2007 poll included a ballot-paper for local councillors, based on the unfamiliar "single transferable vote" method which requires the elector to number the candidates in order of preference. Unprepared and baffled, many Scots scattered their crosses in all the wrong places.

The outcome was that almost 142,000 votes were rejected as incorrectly filled in (85,644 in the constituency vote and 56,247 from the regional list). In a small country where only 51% of the registered electorate turned out to vote, this meant that about 7% of the votes cast were disqualified. If the result of the election had not been so close, locally and nationally, this disaster might not have mattered so much. But when the last declarations had been made next day, and when the final computation of seats was made, the Scottish National Party (SNP) had emerged as the largest party by only one single seat.

In sixteen out of the sixty-four constituency seats, the total of rejected votes was higher - often far higher - than the majority of the winning candidate. Understandably, there are already demands for recounts (by manual counting) and threats of legal challenges under European human-rights legislation. In other words, if only one single seat or list-place changes party hands through a recount, the SNP could lose even the minimal majority it won. It's arguable that the whole election should be declared invalid and rerun. But no leading politician dares to say that in public.

The Holyrood tunnel

So a bungled election leads to a tragic political impasse. Tragic, because this should - even for those who are not tempted by the idea of Scottish independence - have been one of those "glad morning" dawns of change. For the first time in about fifty years, the Labour Party has lost control of Scottish politics - at both national and local level. For the first time ever in its eighty years of existence, the Scottish National Party has broken through to become Scotland's leading political force, the winner of a democratic election.

There is no question about it: the SNP won the campaign, and its leader, Alex Salmond, emerged in the last few months as the most convincing figure in Scottish politics. Equally, it's beyond question that Scottish Labour lost the campaign, putting up a sullen, negative showing under the leadership of the decent but increasingly bewildered Jack McConnell, the outgoing first minister. In contrast, the SNP slogan "It's time" seemed to catch an impatient readiness for change.

But winning campaigns, even winning elections by a whisker, does not always add up to winning power. The SNP now finds itself in a trap. It has no overall parliamentary majority at Holyrood. And its chances of finding enough coalition partners or allies to allow an SNP government to govern suddenly look remote. Alex Salmond is reduced to the prospect of a minority government, living from day to day, at the mercy of its enemies.

In the two previous Scottish parliaments (1999-2003 and 2003-07), the Liberal Democrats were junior partners in coalition governments with the Labour Party. Now that Labour has been defeated, the Lib-Dems are the only plausible partners for the SNP. And yet they have flatly refused all Salmond's approaches. Their leader Nicol Stephen insists that negotiations are pointless until the SNP gives up its intention to hold a referendum on Scottish independence by 2010.

There is something very odd about this. At first, people thought Nicol Stephen was bluffing, trying to raise the price for his support. But he is not. And yet none of the reasons for his refusal make sense.

It's worth looking at the Lib-Dem case in detail:

1. "We are a Unionist party, and can have no part in any independence project".

This is ridiculous for two reasons.

Firstly, because the Lib-Dems are actually a federalist party, not really a unionist one dedicated to the preservation of a centralising British state governed from London. They demand sweeping increases in Holyrood's power over finance, which under the British system would almost inevitably lead towards full independence.

Secondly, the grounds for opposing a referendum don't hold water. If the Scots do want Scotland to become an independent state, then blocking their opportunity to say so is a violation of democracy. If they don't want independence (and at present most do not) then a "unionist" party has nothing to fear from a referendum.

2. "The only referendum that counts is the vote on May 3rd - and by voting mainly for Unionist parties, the Scots have already rejected independence".

This is a quite childish view of politics. "Independence" was not on the ballot-paper, and constitutional matters hardly ever direct people's choice between parties at elections. In Scotland, every politician knows that party loyalty doesn't tell you about a voter's views on the union. For many years, the biggest single block of pro-independence Scots was composed of committed Labour voters - although their party was rigidly unionist.

3. "The SNP won't compromise on their referendum; it's their only policy".

Nobody believes this. Salmond, who originally wanted a one-question, yes-or-no ballot, now repeats that he would accept a multi-option referendum (making an absolute majority for independence almost impossible). He makes clear that the poll could be delayed for years. Finally, he would consent to parking the whole independence / referendum question with a cross-party constitutional convention, leaving the parliament free to get on with normal business.

The convention idea was also in the Lib-Dems' manifesto. Neither is the "one policy" gibe true. The SNP does in fact have a detailed programme of reforms - many of which are close to the Lib-Dems' own. As well as the constitutional convention, the SNP shares the Lib-Dem demands for expanded powers for Holyrood and a local income tax. Labour and the Tories would not touch either notion.

4. "The suspense of an independence referendum would overshadow the whole parliament, making coherent reforms impossible".

There is no evidence whatever for this, especially since it's common knowledge how unlikely a "yes" majority for independence is at the moment. In any case, a referendum has to be decreed by Holyrood, and the SNP - even if it did form a coalition - would probably lose that vote.

The power of suffocation

It follows that, given the feebleness of Nicol Stephen's arguments, there must be some other reason for his stubborn refusal to seek a deal. In Scotland, a rather convincing conspiracy theory is gaining ground. This reports that an ambitious bargain has been struck between the two "big beast" Scots at Westminster: Menzies Campbell, leader of the British Liberal Democrats, and Gordon Brown, soon to become Labour prime minister in succession to Tony Blair.

The terms would run like this. In Scotland, the Scottish Lib-Dems will boycott all contacts with Alex Salmond and instead join an unofficial "unionist bloc" of Labour, Tories and Lib-Dems at Holyrood. The bloc (already nicknamed "the unholy alliance") would treat the SNP ministers as outlaws, despite their democratic mandate. It would oppose and frustrate every attempt they made to govern until the SNP-led Scottish executive collapsed and the minority government resigned.

In return, Gordon Brown would look kindly on the Liberal Democrats if - as seems possible - the next United Kingdom elections in 2009 destroy Labour's absolute majority and produce a hung parliament at Westminster. Then there could be a Lib-Lab coalition at the British level; and - if Brown is feeling especially grateful - some assurance that proportional representation would be introduced for Westminster elections.

And in Scotland, a third Lib-Lab coalition executive would be constructed. The Nats would be shown, once and for all, that they were aliens and intruders with no right to govern Scotland. No referendum would be allowed, and the independence idea would be discredited for ever. End of story, with everyone happy...

Could this frightful scenario really be taken seriously by anyone? It seems that it could. And yet it is not only a democratic disgrace. It is a script for uncontrollable political upheaval at some point in the future. The desire for change in Scotland is authentic. A steady current of opinion is moving towards wider self-government for Scotland, including fiscal autonomy - extensions of devolution which the UK framework and Prime Minister Gordon Brown may be unable to tolerate.

Pretending that all this isn't happening by suffocating its messenger - the SNP majority in the elections - is suicidally daft. The implication is that devolution amounts to a sham, and that the important decisions about Scotland - not just policy decisions but even the choice of which party governs in Edinburgh - are still taken behind closed doors in London. What conclusions are Scottish voters supposed to draw from that?

So Alex Salmond is left with no alternative. It's minority government or nothing. Westminster tradition sees this as un-British. In fact, there were two minority British governments as recently as the 1970s, both Labour. Harold Wilson ran one in the immediate aftermath of the February 1974 elections. After Wilson resigned in March 1976, the narrow parliamentary majority of his successor James Callaghan became ever tinier thanks to a series of by-election defeats over the next three years. To keep the wheels of government turning he had to rely on "arrangements" with the Liberals and - as it happens - the then sizeable SNP contingent to get its laws through. It has to be said that neither was a success story. Wilson gave up after a few months, and called fresh elections in November 1974 which gave him a working majority. Callaghan struggled on, until his failure to ratify Scottish devolution in 1979 moved the SNP MPs to bring him down.

But minority governments can survive, even get things done. All depends on the tolerance and responsibility of the opposition parties. And those who planned the Scottish parliament in the 1990s had a vision of a new sort of democratic assembly, far removed from obsolete Westminster patterns, whose watchword would be cooperation rather than confrontation. Party boundaries would be relaxed and party whips would not dragoon their flocks.

Some of that - although far from all - has become reality at Holyrood. But will the opposition parties remember those cooperative dreams as they close in on the helpless SNP? Alex Salmond's hope, even more urgent than holding that referendum, is to show the Scots that the SNP can govern sensibly, effectively and constructively. It does not look as if he will be allowed that chance.