Rumours that the building is cracking-up began circulating in March when it was revealed that the bomb-blast-resistant windows in the EMBT/RMJM-designed debating chamber had developed 600mm-long cracks.
The panes are merely feet away from the chamber's oak beams which are currently strapped-up after one of the 3m supports collapsed.
But a Holyrood spokeswoman has now insisted there was no basis to the subsidence rumours.
She told the AJ: 'We have not made any secret of problems with one or two windows. We have had experts walk the foundations to check and have never had to commission reports into this.
'Earlier this year, a member of the public claiming to be a buildings expert claimed the cracked windows were the result of subsidence. He chose to go to the media.
'We suggested he raise the issue with the Scottish Executive and have not heard anything since,' she said.
A RMJM spokeswoman added that she was 'unaware' of the cracked windows in the debating chamber.
This is the latest embarrassment to beset the notorious complex which ran ten times over budget.
Last year 150 of the 500 windows in the building's committee towers had to be replaced. Staff were also told to keep paper blinds away from the surface of the glass to avoid heat build-up which experts believe to have caused the cracking.