Hmm seems like it broke saving on the flash cart I was using. Is that possibly because of the bootleg flashcart save changes? My cartridge just uses normal 32KB FRAM and v2 it worked perfectly fine. Does it try to use the bootleg save feature automatically? The save works perfectly in mGBA still and on v2.1.1
Edit: what's weird is it does auto fill my name and stuff out of my old high scores list.
Edit edit: So I've done some testing. On my flash cart it seems to be writing the save back to the ROM and not seeing that there's 32KB of FRAM on board. Is there a way to get a version that doesn't do that lol I don't currently have devkitarm setup on my WSL but I guess I can try messing around with the source if it's not something you want to look at.
final edit: It's definitely an issue with the save to ROM chip code. I think it just assumes if the ROM chip responds to the flash commands that it needs to write to the ROM chip. Which doesn't work in situations like mine where the ROM chip is flashable, but also it has FRAM. It ends up just ignoring the FRAM and writing to the ROM chip anyways. I was able to clone the repository and get the build running on my WSL Ubuntu installation. And just changing the def.h file to:
#define ENABLE_FLASH_SAVE 0
And after that it just works as expected. Hopefully it doesn't introduce any other issues since I'm building it on my machine rather than yours which is untested thus far. I'm unsure how much work it would take to add some logic to the save to flash code for this scenario or if it's just easier to build with that def changed as an option.
Anyways thanks a lot for the great homebrew title! I love it.
This is my cart for reference: 
