If you have a breakpoint in a comment or none-code line, gdb will set it on the next line that has code.
So maybe the breakpoint is somewhere further up in a comment.
Also if you use symbolic links, for the IDE there will be 2 distinct files (even so they are the same via sym link). If the breakpoint is set in either one of the files, the debugger will apply it. But the IDE will only show it in one of the files.