May have found a fix, but not 100% sure.
Use
Shuny to convert a saved file from No$GBA ( I was forced to play on the computer, instead of my DSTT, because of this stupid save issue.) I have 4 badges, saved it, went to this site, converted it to DSTT and put it on my DSTT.
My save file worked flawlessly the first time, so I saved it a couple times, reset and test.
I get to the "press start" screen and it says:
"The save file is corrupted. The previous save file will be loaded"
It has been saying this for the past 40 saves, I'm still not 100% sure if this is a fix, but the saves are fine, and just ignore the message!
Again, not 100% sure, but 40 saves is impressive.