Debugging and Modules

I am not sure if anyone else uses Eclipse for debugging their php, however I am having problems understanding the way that D7 is calling modules for their functionality. I am trying to debug the quotes module at the moment. Out of interest really and I and just seeing how things hang together. I set my break points at the beginning of each php file in the quotes module but when debugging none of the break points are honoured. Any ideas? Anybody use any other debugging packages but not have the same problem? I know that Eclipse will stop at other break points in other files apart from the file I initially start my debugging from which used to be an issue with Eclipse/Xdebug.