Reminds me of a problem I just had with Eclipse's debugger (which sadly seems to be one of the most capable GUI debuggers on Linux).
I set breakpoints and they were ignored.
https://stackoverflow.com/questions/4388192/eclipse-doesnt-s...
One time it was the top answer -- I had "skip all breakpoints" on. How it got on, I have no idea, since I did a fresh install of Eclipse pretty recently.
Yesterday it was still ignoring my breakpoints even though that was NOT on. Why? I have no idea.
So I still debug with gdb when the 'bt' command suffices. When I want to do more advanced stuff, I'll fire up Eclipse maybe, but I'm honestly loathe to do so.
Tooling this complex needs to provide controlled methods for controlling state, both in the tooling and that tooling's impact on the data it is operating on.