Ok I have some questions : When you click Save from the pause menu it brings up the normal Save box? And does it show the other save files? And when you type in a new name and click Save what happens?
OK can you please try running the game again, doing a save, quitting and then send me the resulting log file? you'll find a log file called Autonauts_Data/output_log.txt in your install folder.
Oh and is save also broken if you start a new world?