I remember that it happened in the last version as well, and idk why but my saves from 0.048 still didn't work in 0.05v3.The dev changed versions of Ren'py back at the 0.048 release which caused some users' saves to not work. If the last time you played the game was before the 0.048 release then that might be why.
I usually download a compressed version - maybe someone messed that up the last time.