Help with savestates and regular saves

[MegaDeox]

Hey guys,
I think I need an explanation regarding save states, memory cards and the gci folder.
I'm playing Paper Mario TTYD, and almost everytime I'm loading a save state I can't save properly afterwards (it says the memory card is not the original).
Now, I understand this is a known issue, and it also happens with Mario Sunshine, but I'm wondering if there's a way to make save states work.
I'm using the gci folders right now, but I don't think using a memory card helped.
Can someone please help me understand how to make save states work properly without screwing with actual saves? (If that's possible at all).
Thanks in advance!

[JosJuice]

Once you have made an in-game save, make sure that you don't load any savestates that were created before you made that in-game save. This helps avoid problems, but I don't know if it's enough for avoiding all problems.

[MegaDeox]

(03-04-2019, 06:20 AM)JosJuice Wrote: Once you have made an in-game save, make sure that you don't load any savestates that were created before you made that in-game save. This helps avoid problems, but I don't know if it's enough for avoiding all problems.

I've read that, but it's not enough to fix the issue. Here's my use-case:
1. Open dolphin, TTYD
2. Load a normal save.
3. Savestate once it loads 
4. Exit dolphin and enter again
5. Load the save state
6. Now I can't save normally.