I, too, suspect that the problem is the towels. I have sewn fleece liners and pads that consist of two layers of fleece with a uHaul pad sewn into the middle. I then have puppy pads under the fleece to catch any stray leaks or urine sprayed into the corners...nothing else. The puppy pads rarely display any evidence of urine except perhaps around the edges of the fleece.
With fleece, you absolutely MUST spot clean the cage 2-3 times a day to avoid your cavies wearing "poop shoes" and smearing the poop all over the fleece. A good hand vac is invaluable in this process. One of my cavies is fully litter box trained, the younger one only partially so.
Something else I find helpful is a product called Clean Cage (a Super Pet product). When the litter box is spot cleaned, I spray it with CC and then add a small amount of fresh litter. I also use Clean Cage directly on the fleece as a deodorizer. If you spray it on top, then keep the cavies out of the cage until it dries (fairly quickly). Otherwise, I spray it on the fleece and turn the sprayed side down. By using both sides of the fleece liners and pads, I only have to do a complete cage cleaning once a week. Often change the cozies and the small "area pads" twice a week.
I can easily say that the one MOST valuable aid for the piggy area is an air cleaner. What a difference it makes! I keep one running on low 24/7 almost year round. (doesn't seem to pull much electricity) Good cage hygiene plus the air purifier keeps the piggy palace--and my home office--odor free.