Another “debugging break” is the use of method entry/exit breakpoints.
Did you try to remove all breakpoint definitions once?
Sometimes i think Eclipse is getting out of synch with some of its internal/displayed state. Perhaps you should try to setup a new (not copy) of your workspace. This sometimes helps me to recover from spurious features.
This is how you can remove all breakPoints
Eclipse -> Run -> Remove All Breakpoints – for removing all Breakpoints for all Time
Eclipse -> Run -> Skip All Breakpoints – for temporary remove breakpoints