I too have a similar issue with saving and loading.
I had just been gifted the game via Steam last night. The game does the actions of saving and auto saving, however loading or continuing a game returns me to my room with 0:00:00 time played - a new game basically.
I have checked the files from My Documents > My games > South Park - Stick of Truth > saves and they are there..so my guess is the game isn't grabbing the info from them when continuing/ loading a saved game. Maybe?
Thanks in advance!