It sound like a permission issue. The saves are located in appData, ensure that the windows account you're using to launch the game have writing permissions on that folder.
Gald it's working ! Your second folder probably don't have sufficiant permission to read and/or write systems files. If a game need a specific DLL from windows to launch, it won't launch. The Pacifier Project is compiled as a standalone, thus is can launch from anywhere (in theory) but need access to write save files.