For one, a bunch of tiles on the right edge keep shifting, disappearing, and transforming in relation to how I made it.
Second, those shifted blocks usually are insubstantial. I can pass right through them, even if some of them appear to be in the right place. The tiles on the top, left, and bottom edges of the level are usually fine.
A no, word wrap is not on. No, it's not RTF. Also, I recently beat the game, so I don't want to reinstall on the off chance that would help.
Also notable: The objects are almost always the way they should be.
Here's the latest data I copied from the level editor text box.
Now the before/after.


The only object that seems to have moved is the door in front of the right exit. Also note that there are snipers I had removed in the editor and I am passing through "solid" blocks.