What game? Please provide the Gameshark save.

Pokemon Sapphire
pokemon-sapphire-version.2532.sps.zip

This save is for a US version of Pokémon Sapphire. Did you try it with a European version?

My ROM is the USA/Europe version.

I know the save works with my rom as I tried it with Visual Boy Advance and it works fine.

There is no "USA/Europe" version of Pokémon Sapphire. The ROM site you downloaded it from mislabeled it.

That's what mGBA says it is.

It's Rev 2 that has the berry fix.

Gonna have to yell at some No-Intro datters then. Anyway, it loads fine for me.

E] It does NOT load fine for Rev 2.

The MD5 of my rom is 9bc2b765ca6997175fac51e6cdc29089

GameShark saves do checksum matching. Since the checksum is different, it thinks it's the wrong game and rejects. It's arguably a bug in VBA that it doesn't reject it. This information is not presented to the user though, and there's no option to override it.

As far as I'm aware the only difference in the rev 2 is the berry glitch is fixed.

The file is different. That's enough for the checksum matching to fail. That's the whole point of checksum matching.

There should be an option to override it since it's the right game just a different revision.

I don't disagree. And it turns out I already had a flag for disabling checksum matching, but it wasn't zealous enough with the checks it skipped.