Confirmed;
Just tested it with GDB, and you're right, the dialog remains open even after stopping the debugging (the application doesn't seem to terminate). Even after Force Quit, the dialog remains open.
In a few minutes I'll try LLDB as well.
Sounds like 2 different things?
The original issue as far as I understand is that the "open dialog" is a system-wide-stay-on-top, and as long as the app runs (or is paused, but not yet terminated) the dialog is on top (until one selects a file and presses ok, presumingly).
Your description indicates, that even if the debugger stops/terminates the app, then open-dialog remains?
So then "ps ax" did the app terminate?
Can you check in "debug output" (Menu: View -> IDE Internals / or 1.8.x: View > Debug Windows), if the IDE did send a "kill" to the gdb?
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As for the stay on top:
What happens if you do NOT debug. Just run your app ("run without debug") and open the dialog. While the dialog is open, can you bring any window in front of that dialog.
Also start your app outside the IDE, and check if any other window can come in front of the dialog.