As Labour and the SNP struggled to spin yesterday's local election results, one thing was not in doubt: it was a good day for penguins.

Professor Pongoo the Penguin, aka climate-change activist Mike Ferrigan, picked up more votes than the Liberal Democrats in Edinburgh's Pentland Hills, confirming the LibDems as the pariahs of Scottish politics. They were wiped out in Stirling and lost half their vote in Edinburgh, where the leader of Edinburgh City Council, Jenny Dawe, fell to a Green.

It raises questions as to whether the party in Scotland will ever recover from the coalition with the Tories at Westminster. But the more immediate question is: where did its vote go?

Clearly Labour got a slice of it this time, unlike in the Scottish parliamentary elections last May when the SNP hoovered up most of the stray LibDem votes.

Of course, Glasgow was the big story, as Nationalist dreams of a historic breakthrough turned to dust.

This was a huge psychological blow for the SNP. Only two months ago, at its conference in Glasgow, Alex Salmond had called time on Labour's 80-year dominance of Scotland's largest city. After the SNP landslide in the Scottish Parliamentary elections, it seemed ripe for the taking, with Labour crippled by scandal and division.

Surely the time had come for a change. But no – Glasgow was not for turning. The SNP was crushed 44 seats to 27 on a shockingly low turnout of 32 per cent.

Alex Salmond insists his party did not expect to take Glasgow and that it made significant progress on 2007, which was itself a good year. However, there was no mistaking the disappointment among leading Nationalists at the failure to grasp the glittering prize, or at least break Labour's grip.

I was always doubtful myself – it didn't take a genius to work out that Labour would pour everything it had into defending its citadel, almost to the exclusion of the rest of Scotland. This was an existential contest for the Scottish Labour Party.

If Glasgow had fallen, we would now be saying Labour was in terminal decline and the SNP was now the established party of the whole of Scotland. A victory in Glasgow might even have given the SNP the 'Big Mo' – political momentum that might have lasted all the way to the independence referendum. Instead, people are talking about the SNP having peaked. Suddenly it is beginning to look a very long time until October 2014.

Of course, the SNP did make genuine progress in these elections, increasing its vote. With 424 seats it is the largest party in Scottish local government. You can't argue with the Nationalists taking overall control in Dundee, Angus and, along with the independent Nationalist, Peter de Vink, probably taking Midlothian.

Alex Salmond is right to say it is remarkable the SNP is still gaining at all after being in government for five years. By now, governing parties are normally suffering from mid-term falls in popularity and council elections are an opportunity for voters to express their discontent. Not this time.

But in politics, perception is everything and in this election, attention was focused, rightly or wrongly, on Glasgow. Nor was it just a one-off. Labour also did well in places like Aberdeen and Fife, where they gained seats. Over in the capital, Labour leap-frogged the SNP to become the largest party. This wasn't a purely West of Scotland phenomenon.

So what was happening? Well, take Fife, where the SNP gained four seats, but Labour gained 11. The truth is both parties had a good night, as they feasted on the carcass of the Scottish LibDems. It's just Labour got a bit more of the pickings in a number of areas than the SNP.

Why did the SNP fail to repeat the landslide performance of last year? Well, one way of interpreting the result, which is favoured by the SNP, is its vote is actually hardening for independence.

Ok, they say, in 2011 many people voted for the SNP because they were fed up with Labour. It wasn't about the constitution. Now, one year on, the stakes are higher. The referendum date is set and Scots have spent a year thinking about independence. This means that some fairweather supporters are falling away. What we are seeing, then, is a more positive vote for the party of independence.

Nonsense, says Labour, Scotland is only now waking up to the dangers of independence and realising that the SNP is a one-trick party. That remark by the SNP group leader, Allison Hunter, about Glasgow being "a stepping stone to independence" was the key.

The SNP's momentum is faltering as the novelty of an SNP Government at Holyrood wears off. The Scottish voters gave Labour a good hiding in 2011 but, having made their point, they are returning to the fold in places such as Glasgow, where people want protection from the regressive social policies of the Coalition Government.

Could the controversy over Alex Salmond's links to Rupert Murdoch have played a part? Neither Labour nor the SNP is claiming the First Minister's apparent willingness to lobby on behalf of the tycoon was a factor on the doorsteps in Glasgow. But the issue certainly provided a negative backdrop to the local election campaign, at a time when the SNP at Holyrood is not doing a great deal on the legislative front.

There is a perception, astutely fostered by Labour's new leader Johann Lamont, that Alex Salmond is a bit too big for his boots, a bit too close to wealthy individuals such as Murdoch and Trump, and losing touch with the issues that concern ordinary people.

And if we are talking about the differential redistribution of LibDem votes then it stands to reason, especially in Edinburgh, that the Murdoch factor might have made former LibDems think twice about voting SNP this time. They care about such things as democratic accountability.

It's too early to say, but it may be that, in some wards, it was Rupert wot lost it.