I have a similar issue. My test seems to confirm that my project (that includes other projects also in the cvs) ignores breakpoints _after_ a call to a "other" project. The breakpoints before the "external call" works fine. I am using a two weeks old Gallileio release (Build id: 20090621-0832) on Ubuntu. However, these problems with Eclipse ignoring some breakpoints started a few weeks back, before I tried to solve it with updating my Eclipse. Back then, I was using a somewhat older Ganymede package.
I am not 100% sure what triggered the problems, but I believe a restart during my vacation due to powerfailure at work might be the culprit. Thats just a guess however.
My projects does not use swing, or apache. Its pure java / ant run from inside eclipse. Everything seems to work fine from code point of view. I have tried to clean / rebuild and conditional breakpoints and all sorts of things I could come up with, nothing helps.