Hm, they should work, but since they're not I have an alternate solution. Use the Goomba Frontend with the latest version of Goomba Color to create your own compilation containing all your *.gb/*.gbc games. Then follow these instructions to inject each game's save file into the compilation's *.sav file:
1. Get the save file for the original game (I'll use Pokemon Red as an example), which will probably be between 8 KB and 32 KB
2. Rename it from *.sav to *.dmp.
3. Open the Goomba Color compilation in VBA and select Pokemon Red to start the game.
4. Open the memory editor (in the Tools menu).
5. Click the Load button, then select your *.dmp file. For the address, use 02038000. The size will be grayed out but should be no larger than 8000 (hex for 32 KB).
6. Close out of the memory viewer and press L+R to open the Goomba Color menu, which automatically updates the *.sav file with your injected SRAM save.
7. Restart the game (or VBA entirely to be sure) and see if it worked.
Do this for each game. I know it's a tedius process, but it's the only thing I can think of.
Instructions adapted from
http://wiki.pocketheaven.com/How_to_exchan...mulators_and_PC with additional comments based on my own observations.
EDIT: Note that you will need to patch the compilation with the Supercard patcher before placing it on your card. I usually use nothing but the first save patch and then use the QPC method to save, though I've heard that you can successfully patch it to use the L+R+A+Select button combo.