I would assume they calculate it based on the rates when your fixed rate ended, rather than when you first took out your tracker (i.e. 2006).
Although I am not sure that is actually what they will do, especially if I am offered ECB plus 3.5%. My fixed ended in August 2009 and at the time PTSB variable rate was 3.65%, and the ECB rate was 1% - which means a margin of 2.65%.
I would be interested to hear to know fixed rates they were offering back then as well.