gdbstubs

Could the fact that I have interrupt vector management in multiple places be causing me problems with interrupts. I am reasonably sure that I
not getting interrupts at all in my main code. Is this because the interrupt vectors being used are those in the stub and not the main code.
Does this mean then that I should link the stub in with my main app, blow this to on-chip flash, run from there but would be able to attach gdb to it and run like that?
I also have the problem that when I modify the SR to set the interrupt mask to 0 for external interrupts, I get an illegal instruction error. I am very confused.

James