So, I'm not sure where the issue was happening, but removing my PlayMakerGUI solved the issue.
This must've just been some random bug because it only occurred in one of four (mostly) identical builds. All the builds had the PlayMakerGUI, but on a hunch after digging through lots of issues with Cursor.lockState I tried removing it from the one problem scene and voila...
I sincerely hope this may help if anyone is having similar issues. I spent many frustrating hours on this one.