I've had a similar problem. Flash Builder shows me the current source when debugging, but when you try to step through it, it is obviously running a previous version of the source. What fixed it for me is to switch to another project in the workspace, compile it, then return to the main project, and recompile the modules that were screwing up. Hope that fixes it for you too.
Interestingly this problem seems to only occur on my new Windows 7 system with the latest Java. My older XP system would crash when running out of Java heap space, but would never go out of sync.
