Well, I feel very stupid right now. I had previously checked my device manager to see if any other devices were showing up there that shouldn't have been. Everything looked fine to me so I moved on.
I have a joystick on my desk that I thought was not plugged in as I have not played any games that use joysticks for a long time, so for the hell of it, I checked behind my pc and....lol. Of frickin' course it was plugged in. I unplugged it. Problem seems to be gone for now. I think the joystick was flagged as something generic like "USB Input Device" or "HID Compliant Device" in my device manager, so I assumed it was just a driver for something else.
I'm still very confused why this problem only occurred after cutscenes and I otherwise had no issues (would have thought the joystick would have interfered all the time), but I am willing to let that mystery lie for now lol.
Thanks for the help guys. This should make future playthroughs a lot smoother for me.