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I have extended CDT to launch a configuration consisting of multiple targets. This works fine, but when I set a breakpoint on a source line that is available for all targets, the breakpoint is sometimes fail to be set for all targets. The code first sets the breakpoint on all Targets. After this, depending on the timing, it sometimes remove the breakpoint from one of the contexts. This behaviour seems to be caused by a thread synch bug in the CBreakpointUpdater in CDT.
Can you try it with the latest build? Major changes have made in CBreakpointManager in RC2 to prevent the UI blocking.
I've added bug 289915. I'm not sure, but this could eventually be the same bug. This bug is quite old and there have been a few changes since. However the description "The code first sets the breakpoint on all Targets. After this, depending on the timing, it sometimes remove the breakpoint from one of the contexts." matches the issue I fixed in bug 289915.