Everybody knows ball bearing slides run better with a few missing balls Steve 🤣  The good news is that you found the culprit pretty quickly and you don't have to spend months trying to run down an unknown problem.  FWIW, I'd leave the enclosure.  Dust is the arch enemy of machines with ways/slides and bearings.  

It looks like the carrier is bolted into wood?  I can't tell from the pictures but I assume there are threaded inserts in the wood?  In either case, I think I'd swap the wood out for MDF.  It's a lot flatter and a lot more stable.