dhoyle,
First I would suggest checking your log file (<workspace dir>\.metadata\.log) for exceptions pertaining to the breakpoints. Then I would try and figure out what changed recently (did you upgrade from 3.1M4 to 3.1M5a or something?) that could cause this. Then I would try and shut down Eclipse, add ‘-clean’ to the command line args you use to start it, and restart it. This will allow it clean out its cache and rebuild it. See if the breakpoints work.
Then I would subscribe to the Eclipse newsgroup and ask there, not because we don’t want to help, but because I am out of ideas 😉