The problem seems to be worst if those breakpoints have conditions or commands attached to them, but I've seen ungarnished breakpoints have problems. The most common thing is for the process running to segfault.
This was caused by do_syscall accidentally saving registers in the thread structure when the SIGTRAP it was looking at was caused by a breakpoint rather than a system call. That state was restored instead of the real process state when the system call exited, causing all sorts of problems.
The fix is in CVS and in http://sourceforge.net/patch/?func=detailpatch&patch_id=101646&group_id=429
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