The first question that comes to mind is - what, if anything did you use on the floor to take care of the flea problem? Maybe it is something that kills fleas AND repels cats. Since cats are very sensitive to smells - maybe some odor in the rug is keeping them off the floor and away from the litter box.

For the areas where they've already gone, get a Rug Doctor bottle of enzyme cleaner to take the smell out, then treat the areas w/spray to repel them from going back. What has worked for us too, is to keep an aerosal bottle of water out & when they head back to the areas they've previously used, spray a little water - they don't like the sound or the water! GOOD LUCK!