Hello- Not sure if you'll receive this as your post was made in June, but here's my two cents--
Nintendo doesn't want anyone to use anything except Alkaline batteries in Gameboys--and they will promptly void your warranty if you call and tell them anything to the contrary. Nintendo policy.
Between my wife and three kids, we have 3 GBA and 2 GBC platforms. The GBA's all have Afterburner lite kits, and all five use rechargeable external battery packs. All of the packs, even the ones for the GBC, have solder-tab style NiMH batteries inside. I know this as fact as I've had to replace a few of them about three months ago.
Wally-mart sells Rayovac NiMH batteries--try a set. Only thing I would avoid is trying to charge them in the Gameboy. Unless you buy an external pack, I would pull the batteries out to recharge them.
Good luck!