Hi rekisum,
I observed that if you switch between different CB projects then sometimes the working directory is not correct, but I did not find a way to reproduce it. But perhaps this could be your problem. Just use the command pwd in the debugger to see if the working directory is correct. You could even force the debugger to use a certain working directory with the comannd line option --cd=<workingdir>. This fixed my problem with an external debugger.
Bye,
Mario