Version Control assets missing

So this is the well-known assets missing (like, Unity sets them to 'missing' despite the files still being in the same place) after pulling bug, and I tried practically anything that was suggested to fix it. We're using Git and Unity 4.6 beta.

I did:

• Enable visible meta files
• Set asset serialization to 'force text'
• Properly setup my .gitignore file ( http://pastebin.com/3jzF3kMi )
• Checked meta file guid (they were identical everywhere)
• Delete my (and my teammates) Library folders countless times
• Recreate the entire git repository

But nothing worked. Basically every time someone pulls changes a lot of things break, an animation gets unassigned and a certain sprite gets the same treatment in all prefabs it's linked to. These are always the same assets.

 

Gonna bump this. I think it might be a bug in the latest Unity beta since I had no issues prior to updating. I will be reporting it, see if Unity QA can reproduce it.

 

I'm still getting the problem. Here's some more research:

If a teammate commits the scene, the FileID for the sprite is 21300002, as is described in the meta file.
However, with this FileID I get a missing sprite error and when I go ahead and fix it, the file ID in the scene file is changed to 21300000 which *should* point to a different subsprite according to the meta file.

It seems that on my computer, it doesn't look at the meta file for the file ID at all.

Clean checkout or Unity reinstall, nothing fixes the problem.