Flash builder profiler not working has been like a thorn in the flesh for a long time. After trying out multiple options, right from installation and formatting and blah blah… nothing worked properly. Strangely it was working on few user machines and we had no clue as why flash builder is behaving in irratic way. The problem was mainly with Domain user accounts, as it was working properly for local accounts.
Finally I stumbled upon following link and got a clue… and it worked too !!! 🙂
Check the posts about home drive settings.