Here are a couple of ideas.
1. Make sure the Build Option is set to Generate source code browse information, then recompile the file and try a breakpoint.
2. Is the .c file excluded from your project and its .obj file included? Excluded files are shown grayed-out in the project window. Toggle exclusion by highlighting the file name in the project window and pressing Ctrl-E. You can't break in an object file.
3. Are you sure that functions in the c file are being called? In a c file in which breakpoints work, set a break point on a call to a function in the c file that doesn't stop on a breakpoint. At the working break point, step into (not over) the function call and see where you go.