TENS of thousands of rejected ballot papers in the Holyrood election and computer breakdown threatened to throw the Holyrood and council results into chaos early this morning.

In the relatively few results that were announced through the night, the SNP vote surged, but without a collapse of Labour's support. Alex Salmond and Nicola Sturgeon were among the SNP's most high-profile victors in Gordon and Govan.

Labour leader Jack McConnell was the first MSP to have his result declared last night, winning Motherwell and Wishaw despite a 7% swing to the SNP.

Rejected and spoiled ballot papers were running at around 1000 in most seats, and as high as 1850 ballot forms in Glasgow Baillieston. The problem could have rendered around 75,000 votes invalid, and that dragged down the official turnout figure.

Concerns about the reliability of the count follow protests raised over recent days about delays in sending out postal votes. The controversy is linked to redesign of the Holyrood ballot form, and possible voter confusion with the radically changed voting system for councils.

Apart from those problems, the Western Isles count was delayed until 10am due to problems in flying ballot boxes from Barra to Stornoway.

Although the change in voting forms was disputed by the Scottish Executive, the decision on it lay in Whitehall, and Scotland Office minister David Cairns insisted on going ahead. Ministers also ignored widespread advice to split the day of the Holyrood voting from the new-look council elections.

Mr Cairns said last night the Electoral Commission will have to look into the problem, and Scotland Secretary Douglas Alexander said he had already asked the election watchdog to look into postal vote problems.

Mr Salmond, having gained the Gordon constituency from the LibDems on a swing of nearly 6%, said the decision to run two electoral systems on the same day was wrong.

He was heavily critical of the postal voting arrangements for the election, describing them as "totally inadequate".

He added that the decision to conduct a Single Transferable Vote (STV) election at the same time as a first past the post ballot for the Scottish Parliament was "deeply mistaken". "As a direct result tens of thousands of votes across Scotland have been discounted this evening," he said.

"That is totally unacceptable in a democratic society."

"With the SNP gaining seats, he went on to say: "There is a wind of change blowing through Scottish politics . . . a new politics is dawning in Scottish confidence."

SNP results were patchy, failing to take its top target of winning Galloway and Upper Nithsdale from Tory Alex Fergusson, or the number three target of Labour-held Cumbernauld and Kilsyth. The gains from Labour included Dundee West while holding Dundee East, making it the first all-Nationalist city. Deputy leader Nicola Sturgeon won Glasgow Govan from Labour's Gordon Jackson, its first general election win in the city. Willie Coffey won Kilmarnock and Loudoun from Labour's Margaret Jamieson.

Tricia Marwick gained Central Fife from Labour's Christine May, and Bruce Crawford came from third position to take Stirling from Sylvia Jackson of Labour on a 9% swing.

Tory Deputy Presiding Officer Murray Tosh failed to win his party's top target of Dumfries, which remained with Labour's Elaine Murray.

The LibDems had a disappointing night of results. Although they gained Dunfermline West from Labour, they lost Gordon to Alex Salmond and both their Borders seats were in doubt.

Labour faced SNP swings ranging from 4% to 15%, in the case of the Airdrie and Shotts seat where Labour faced pressure over changes to Monklands hospital services but still won.

Labour's majority in Glasgow Kelvin was slashed to 1207, and in Glasgow Anniesland, held by the late Donald Dewar, there was a 4% swing from Labour to SNP.