Anyway, I've run into a few glitches: I also had some weird issues with the Cave of the Eidolons. I was fighting a big formation of warriors and fiends (?), and I think it was after one of them cast charm on me and suddenly Palom had two call commands and about 50 holy claws, but no fight command to use them with
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Also some issues in the sealed cave: I had Edward die to a trap door and then he hid after he was revived which soft locked the game.
I can't confirm exactly what happened or whether it went down like this, but it seemed like when I fought Milon (the first fight), he died on his own rather than from damage. He did hit himself with condemned after it reflected back on him, so I'm not sure if that did it or if I just missed the final blow...On a second try to see if I could replicate it I also just had the game freeze when fighting the first Milon, but I don't remember what happened before hand to do it.
Lastly, I tried using Pray on Mt Hobs and it always seems to cast a mass death spell on my party (once it did Stone but that didn't do anything). What god is Rosa praying to and why does it hate her?
Edit: As I'm sure if often the case, the problem may be a dirty rom since when I checked it was not the same one you have listed in the readme. I'll try again with the new one and see if that fixes any of the problems, and let you know if that works.