I'm using v2.9 b2 and apart from the "Engine is working on Actors" bug which is still present I have experienced the following problem also.
I uninstalled my previous version and downloaded and installed the fullreg file. I didn't manually remove the covers and the like but I did take a backup for safety reasons. Now, some of my movie entries (around 5 out of the 113) have no cover. The files are present in the folder and actually if I go to the cover manager I can see them but first slot is empty. If I click on the second one and then on the button to movie it to the first position nothing happens!