Is there an update regarding this issue because I'm experiencing the same thing. As soon as I try to use my own Makefile I can longer debug and breakpoints don't get hit. The actual error message I get is:
Debugger name and version: GNU gdb 5.2.1
No source file named C:/source/qt2/main.cpp.
I'm using Qt, so if I don't use the custom makefile, I can debug, but then my resource files don't get included properly. Kind of a catch-22.