That could definitely be contributing to the problem. I use fleece in my bunnies cages and runs. I think that makes it easier for them to determine litterbox from rest of cage. Is your bunny spayed or neutered?
I use litter (woodstove pellets) in my bunnies litterbox, and their run floor has plastic protecting the carpet- so I lay a fleece blanket over that- and place the litterbox on top of the blanket to help hold the blanket in place. I also have a dog crate set up as a cage while I am bonding the bunnies- so I cover the cage tray with fleece and the second level that I added has fleece also. I have had good luck with fleece since any nibbles just tends to create little holes. Towels seem to get really ragged looking with long strings, etc and just do not work as well with my bunnies.
I used fleece even when I was littertraining first bunny before her spay and she seemed to get there was a real difference. Now that I am bonding I do get some occasional wee spots- but I just throw the blankets in the wash. They are pretty much bunny blankets only now- but that is OK.