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That's weird - can you double check that .meow files are being created in the installation folder when you save?
Did you get any warning messages about saves when you started the game?

The files are being created, but there is a message on the starting screen about the flashplayer temp files. The config is set to allow.

When in the game, the autosave is there. Just my manual ones aren't.

Ah, yes, temporary Flash files are being blocked for some reason.
It's possible that you have that allowed, but only up to a certain size - worth checking in that Flashplayer options menu if you can increase the file space allowed.
It's also possible that some other application is interfering, maybe an antivirus, Windows settings, or PC-cleaning utility is blocking all Flash files, in which case it may be tricky to figure out what exactly the problem is. Sorry about that.

Don't know if this helps, but when opening the game it works as if I'm opening it for the first time. After starting a new game and quitting, the auto-save reads the old file with only the medals missing.