Nope not spite, your kitty like the the towels better than the litterbox. Cat's are very particular, if their litter box isn't up to their specs they'll find someplace out to use. Try a few things, if it's a covered box- take the lid off, keep nice clean litter in it- they hate the smell of dirty litter same as we do, try a different litter- it may be a texture thing, your kitty may like the felling of the towels butter than the litter, so try a different type.
I would still take the lid off the pan.. Have you smelled in those things?? It holds the smell of pee like you would not believe!! Its awful.. We used to have them when the pans were inside, but once I realized how bad it was I couldn't stand to do that to them.. Still have the pans, just tossed the lids.. Plus, cats like to see if anything is coming at them while they potty.. Maybe the kitty is nervous about another cat or a dog??