i have read the topic about this "bug":
http://forums.codeblocks.org/index.php/topic,4850.msg38322.htmlsince its a gdb issue, there is 2 things that can make things work:
-setting breakpoints using the filename only, the problem is that if there is 2 identical files in the project, gdb set break on the first he'll find
-using "info sources" command to find the proper file path that gdb use
it is not very clean but will work perfectly (and only breaks that return "no source file named etc.." will do that)
i have read that the last one was the best solution for gui, i don't know how others handle that but that would be nice to get it work properly
i hope there is no more problems like that with the last versions of gdb, it's disapointing to see this debugger having that kind of issue ;(