J.D.
This can be a hard one to fix. I was actually told to take the lids off the boxes, because the less dominant cat may be fearful of going into a covered box because he/she may be attacked. Are all of your litter boxes next to each other? We were also told to place a few boxes throughout the house to make it convenient for the cat/cats.
We went out and bought a diffuser from Petsmart, I believe it was called feliway? It was a little pricey, but WELL worth the money! It releases pheramones for the cat, and it made a HUGE difference for our cat! I was also told by someone who works over at the Huntley Animal House that they use those in their cat room so the cats don't get stressed out. Good Luck!