I was playing your Dragon Spirit patch on my STe and about 5-10 mins of play the game saved twice all by itself and then just sat there.
It wasn't frozen though, I was able to hit * to quit.
Automatic save happens in case of some error - like bus error or corrupted RAM. I set it for easier tracing of bugs, errors.
I played this version 3 times completely. No errors happened at all. Possible that your STE works not fully reliable.
Will update Lethal Xcess with HAGA soon ...
Or maybe I had played a couple of other games before Dragon Spirit... Maybe something in memory caused the problem.
Thinking back, I had tried a few other patches before the game with out rebooting or power cycling the system.