Hey, not sure I fully understand what's going on with the save nor do I have a good solution besides loading a hard-save, not using the autosave. Seems like a very unique problem, I've never had anyone report a problem with loading their saves besides just forgetting to save and wondering where the auto save is.
Are you perhaps pressing the quick load button or Q.Load? Because I believe that always loads the autosave. You have to go into the menu and manually pick your save.