You are right, B4J does not have "unfiltered" logs, only B4A does...
So, if I understand correctly, first run is OK, but subsequent are not, right?
What libs are you using? How are you "terminating" your first debug run?
My best guess is that you are using some lib that keeps a hold on some process and therefore, when restarting your app, the process is not re-started as it should