Unfortunately, I haven't had a need to play VC games, so I can't help you with your problem as good as other people may. You might want to check this out though (copied from samiam144's amazing guide) and I'd check out the patched AGB FIRM that's linked:
"DSi/GBA/NES/etc. support
The
patched AGB_FIRM is no longer needed (although in this guide, we already had you install it just in case
DSi games can be ran through sysNand, and reportedly emuNand as well. Install to sysNand to play them in sysNand; install to emuNand AND sysNand if you want to play them in emuNand. DSi cias must be installed to NAND destination (if using FBI).
GBA games can be ran through emunand, or sysnand. They still have to be installed to both emunand and sysnand if your nands are unlinked! GBA games should be installed to SD (if using FBI).
Personally I just install them to Sysnand and play them from there."