If your "cover art stops displaying and reverts back to a snapshot of the movie" and you had Create thumbnails for videos selected, I would assume there is some connection. I expect deselecting that will stop screen shot thumbnails from being created. But that doesn't explain why that was happening when there was already a thumbnail.
Are you using PvdImport? If so, how is it configured? I wonder if the import of a poster (even though one already exists) is triggering Auto-Import to update the thumbnail, but then it instead creates one from a screen shot because this was your preference. When you run PvdImport, do you run a "mass update" on all your videos, or do you use Send to to just update those that need updating?
Have you configured PVD to create and save screenshots in it's database? There's a deficiency in the current version of PvdImport in that instead of exporting a specific poster, it's actually exporting one image at random. If you are saving screen shots in PVD, that image might be a screen shot instead of a poster.