I still don't get why you all are having issues...as I said, I'm using the migration assistant to just put my old system onto any new mac I ver bought....that old system is like 8 years ols...no problems here
try Xbench to see what it says about your system performance and hard drive speed.
did you try completely formatting your HDD, as in not just a writeover but that it'd write zeroes on top of all the files? if not that could also be the root of your problem.
Lasse, you're talking about migrating an old system to new Macs, not problems with a single computer.