When I save a game I see the file being written to the Saves folder, but nothing appears when I go to Load a New game. There's also no visual indication that the game was saved (nothing to click on).
Very strange, try starting the game as administrator.
If your version is 003, saves are path in "C:\Users\<username>\AppData\LocalLow\GGames\Two Sides - Redone\Saves"
Running as Administrator didn't help. :(
Oh, and I am on version 0.02.1
In this case, the files must be inside the 'Saves' folder, which must be located in the game's main folder.