Every asset, all of them, have no history before v13, right?
Well, I dont' necessarily mean a PRJ, but some asset has got somethign weird in it. These are the ones that had teh strange folders showing up, right. maybe they got something else buried in them.
Do that. get one to render badly, swap in some simple object, delete your models, Save everything in a PRJ. restart A:M test that to see if it still renders bad and if it does post it.
An example that does it will get it cleared up fast, just like with the phantom folders.