I used a small ant task after a compilation in Flash Builder. That is done pretty easily with the builder feature in eclipse.
Basically this worked fine, but sometimes it was not executing the ant task. The ant task was also not executing when started manually in the ant view. As this task was just for convenience I never found the time for investigating the problem further. Now for some other task where it is essential to get it run, I needed to find out why it seems to behave instable.
I am not totally sure if I found the real reason (there are some bug reports around this topic if you google for it), but at least I could manage it to make it working again. I suspect that when switching the workspace in Eclipse you need to set the ant home path newly (>preferences>ant>runtime). I did this when comparing the differences between a working Eclipse instance with a non working one. After changing the ant home path to the other Eclipse installations path (I use the ant directory inside the plugins directory of your Eclipse installation), it was working fine. After changing it back to the original path it was also working fine. So I assume that the ant home path got somehow corrupted when switching the workspace (or for some other reason), after setting it again, it seems to solve the problem.
Nasty stuff, but after a long search for the problem I am glad to get it (hopefully) running stable.