Add files/folders in compiler

When I switched from 2012a to 2012b, the compiled program was no longer able to find files that I added using the 'Add files/folders' function on the Package tab. It appears to be able to find them using the 'Add files/folders' function on the Build tab.

Am I doing something wrong? Why can't I find any discussion of this in the documentation. If 'Af/f' on the package tab doesn't work anymore, why is it still there?