So, I looked for any copied .ini files in my data folder, with none to be found. That being said, temporarily getting rid of the contents inside the vis and precombine folders seems to have fixed the issue. My only question is, what's the catch to having removed those files? I'll keep them saved for the time being until I know for a fact that I can safely delete them.
Removing them may cause white void and/or objects flickering in and out of existence in the cells that those files are for. But the problem is that precom/previs is highly personal, depending on your modlist. Remember the last mod loaded wins, so if you have two mods that affect the same area and they both provide precombine data the second one loaded overwrites, and often breaks, the first one. And honestly even if it's not a mod conflict sometimes the precom/vis data included with mods is just bad or incomplete.
In theory you could load all of your mods in the CK and generate new precom and previs for everything so you'd have a nice set specific to your set up. In practice the CK would likely crash before it ever finished.
For now I'd go ahead and keep those files removed, play, and see if you run into other problems.