Interesting. I installed PyDev 1.3.8 into a new/clean install of Eclipse 3.3. Was getting an error (running Trac), so created a project in Eclipse, placed a breakpoint on the line in question and ... the program did not stop on the breakpoint. Do not know why. Did not have time to investigate further. Had to forcibly terminate Eclipse (this is on Linux - python instance under the debugger would not stop). Removed PyDev, and went onto other things.
I know this is not very helpful, but it does sound not-dissimilar to what Markus reports (debugger not-stopping where there should be a breakpoint).
I am still experiencing problems with the Jython Debugger of PyDev 1.3.8. I cannot step into a subroutine which renders the debugger almost useless.
Seems that the problem reported here ( http://sourceforge.net/tracker/index.phpfunc=detail&aid=1662822&group_id=85796&atid=577329) still persists.
Can you confirm this for your installations or do you have a working constellation of Jython version,PyDev OpenSource and PydevExtensions?
Or is there a workaround for the problem?