I provided him with all the files and asked: what files do you see, and he answers a maximum of 1-2 out of 20
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I have the same problem. Nobody has given a good answer so far.
Hey, we are aware of a bug causing this, and are working on a fix!
In the meantime, starting a new Composer session should resolve things.
@danperks - Starting a new composer window does not make any difference 
Can you send a screenshot of this over, so we can see what is happening?