Emulator

If you make a savestate and then load that savestate without making any regular save in between and without restarting the game, does the problem still happen?

Yes, it'll still make any subsequent saves fail.

Probably something about the load state isn't setting card state correctly

Switching from GCI Folder to Memory Card makes it possible to use save states and save files.

Hmm, I was actually testing against this on desktop and observed the same issue there. The pattern is pretty specific though in what triggers saves to fail. Essentially, save states will work only if they are from your current "session" of Dolphin in which you loaded the game. If you load the game, make a save state, and reload that state, it will still work. If you close Dolphin, then start the game and reload that same state, saves will break.

I noticed that running the game with all the debug logs turned on, it was reading memory card blocks 0-4, and 350-351 when it was displaying the error message (checking the header probably).

Verifying what knightmustard mentioned, it does appear to work using a raw memory card, so the issue appears specific to GCI folder saving.

Star Fox Adventures (GSAE01) has the same issue.

1. Make a save state in-game
2. Save in-game
3. Load the save state
4. Save again, the game will say it's not the same memory card

Or:

1. Make a save state on the title screen
2. Load a save file
3. Save in-game
4. Load the save state
5. Try to load the same save file; again the game says it's not the same card

I assume it's because the timestamp doesn't match?

You can use the debug cheat code to skip past the opening scenes to be able to save right away: https://tcrf.net/Star_Fox_Adventures#Chapter_Select

btw that's on Dolphin 5.0-11200 and not using a GCI folder.

PLease try this build: https://dl.dolphin-emu.org/prs/pr-8476-dolphin-latest-x64.7z

It may fix this issue.

The issue reported by Rena is just the usual problem that most games have with saving after loading a state that's older than the last memory card save. There's no way to fix that unfortunately, all we can do is just tell people to not do that.

As for the original issue report, this game actually will refuse to save even when your state is newer than the memory card save. This seems to happen if your SRAM has changed since the save state was created. This PR may address that issue: https://dl.dolphin-emu.org/prs/pr-7396-dolphin-latest-x64.7z

Could this not be fixed by including a snapshot of the SRAM in the save state?