List of breakpoints is empty
This is the breakpoint window? From Menu: view > debug windows > breakpoints?
There is no setting to disable this.
This indicates that something between the IDE and gdb went wrong.
It depends when exactly you got that error.
It can happen when you remove a breakpoint, at the exact moment at which it gets hit. This is very rare. And then you close the window, and all is ok.
If it is not that, then I dont know. Maybe a problem in gdb...
Can you reproduce it?
If you close the window, does it keep opening again?
http://wiki.lazarus.freepascal.org/GDB_Debugger_Tips#Log_info_for_debug_session