Thanks for your answer.
I just noticed, that I used a quite old version of c::b on my dektop-pc (the one, that shipps with the distribution, the nightly build was on another machine, where I did not try to debug this project). Nevertheless I tried the actual nightly build of the debug branch, but there occures the same problem: No "communication" to gdb, while it the programm is running.
I'll see what I can do to provide an example. As I mentioned it worked with a very small programm using custom makefiles. Also possible, that the problem is not connected to the custom makefiles, but to anything else :-/ Debugging from the shell via gdb works like a charm.