How about trying
this?
"...on Windows 7, the solution was to right-click on the Machinarium BOTANICULA short-cut (or exe) and go to 'compatibility mode'. Under this section, turn on 'Disable display scaling on High DPI settings' (the bottom option)"Or maybe you need to make a selection in the "Run this program in compatibility mode for..." option? ( try selecting XP maybe? )
I know it doesn't sound like these suggestions should work but give them a go anyway just for the heck of it. Other than messing with those EXE properties I'm sorry but I can't think of what else could possibly be causing such abnormal behavior in your saved games functionality.