That's crazy. Are you using "Optimize Storage" in Photos?
The ultimate fix would be to backup your current Library, and then create a new one and let it automatically download your pictures from iCloud Photos. You'd have to set the new empty Library as the System Library in Settings>General, and then connect it to iCloud.
But I'd try these things, first, probably in this order:
- Restart the computer (of course)
- Re-start in Safe Mode. This bypasses certain potentially disruptive processes. Safe Mode is different for different computers, so see this:
Start up your Mac in safe mode - Apple Support
- Make a new user and see if the same problem recurs with it
- Use another library if you have one, or make a small test Library with a few pictures in it and see if the same thing happens. You can create a new Library by closing Photos and then option-clicking on the Photos icon.
- You've already repaired your Library, but if the previous steps don't provide any relief, you could try it again after: Rebuild your Photos Library--close Photos and re-launch by option-command-clicking the app icon.
The idea is to find out if the problem is with the Library, with your account, or with caches and login items, and stuff like that. One of these steps may fix the problem, but their failure to work also helps figure out what's happening.