Now the game saves both to program directory, and AppData, if it can't find the one in program directory, it'll try to find the one in AppData as a backup, it will prioritize program directory first tho.
That was fast. At first I thought it was the unzipped location or folder name or something like that. But since you changed the save mechanism, I tried with fresh data.
A warning about the save game location would have done the trick. But doing it like renpy does it, is of course better.