No, I always overwrite the current version. If I delete my version, my saves will be gone, won't they?
No, saves are stored in another folder.
%APPDATA%/RenPy/
Ok, no idea why this would be different, but deleting the old version and freshly installing from the packed file did the trick.
It was because I packaged the game differently this release so it had a different folder structure. Seems as though the older script files weren't overwritten.
One tiny thing. When I go to Club Naughty it still says it's the end of 0.2.6 even tho I'm on 0.3.1 ;-)
that would be because nothing has happened there since so the script for that area hasnt been updated