Just in case anyone is still wondering, I think lots of cards (I've never heard anyone brag about how well SA works) have problems with Sonic Advance. Mine would save up to a certain point, as in, up until a certain number of stages were cleared by the characters and pick-able from the level select menu.
Then after that, nothing. Kind of like if you picked a savetype of the same style but a smaller write size.
My card auto picked the save type when it was written, and it told me it was using the right one. 512 eeprom. I went through several dumps and decided not to bother anymore. I ended up buying the game again, as I had lost it before I even knew what a flash card was.
My suggestion: use an emulator. Works fine on those. I would also test it on another card, if not for two things; one, I don't care about Sonic games much, and two, my other 512 eeprom games work fine.
Oh, and I know the same type of problem will probably occur in Sonic Advance 2 as well. Does on my card at least.
Edit: And the SRAM patch didn't fix it for me, so don't expect much. In fact, GBA Tool Adv only really helped me getting 2 games working that otherwise wouldn't.