I wound up submitting this issue to Apple. Their response was unenlightening, and talking about possible optimizations, updating meta data for new version of Xcode and the like.
I tracked 100 versions from clicking off and on the file. As Apple said, it was “optimizing” every time, but each time it simply moved some XML tags around. Never happy with it’s own optimizations it moved them around the next time they were opened. I’d consider it a bug with Xcode, annoying, but mostly harmless.
This only happened with old XIBs and either moving the contents into a new XIB file or (what really happened) Storyboards got rid of the issue.