Set the savetype to EEPROM 64k, activate the bypass cheat, then reset the game using the File-menu or simply Numpad *, and THEN the game should save and load normally. And yes, apart from setting the savetype (if you saved that one), you have to go through that routine every time you play.
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No$GBA Quick FAQ:
Q1: Savegame doesn't load.
A: Set correct save type. Look
here, divide by 8!
Q2: "Cannot Read Data" error
A: See above!
Q3: Snapshots?
A: Only work for GBA games.
Q4: NDS linking, NDS with GBA slot, Picto-Chat, trading, ...
A: Not yet available.
Q5: When do we get a new version?
A: We don't know. Martin won't tell.
Q6: Donation down?
A: Yes, and we can't do anything about it either.
Q7: Game stops without appearent cause.
A: Turn the Sound option on.
Q8: No$Zoomer fixes don't work.
A: They do only with 2.6a.