I've been using a mix of savesates and in game saving in my playthrough

About halfway through the game I relied on savestates a lot more and didn't save in a pretty long time. When I finally did save the game would just freeze on saving a lot of data and the audio would just be playing a continuous note while the saving icon clock would spin a lot faster, like I've sped up the game or something.

If I load my previous in game save from the menu the game lets me save just fine, so I think the problem begun after that point somewhere, maybe it's got something to do with the savestates. I haven't downloaded or used any cheats or changes any of the settings in any folders. Any ideas on what I can do to fix this?

Edit: I'm using version 0.9.11 64 Bit