At first confused by dates...then realize you're European.
Looks like it's saving to the right place but your prefs.prop has forgotten about all of your other saves. Which means you need to restore your previous prefs.prop.
First, copy from your backup and overwrite that save folder completely. Remember not to change your backup, though.
Then check your prefs.prop and see what the date is on that. If it says anything between 28/08/12 and 01/09/2012 then it's been updated to ignore all of your saves and from now on will save new games and overwrite the old ones in order counting up.
To hopefully fix this, right-click on prefs.prop, click "Properties," then click on the tab called "Previous Versions" and then pick a version of prefs.prop from before the Episode 3 update (at least several days ago, preferably up to two weeks ago).
This should force your prefs.prop to start counting up from your last autosave (55) and recognize all of your previous files.
Restart, check your stats, and try starting a new Episode 3 game with a previous save to see if your choices carried over.