I remember an insightful thread a while back that compared the amount of urates and turds they found when they changed from one substrate to newspaper. The newspaper didn't absorb the mess as much so it was clear when there was something nasty left behind. I use aspen and I think it tends to absorb quite a bit, so although the cage looks clean (from spot cleaning) the bedding is still probably pretty nasty. I would continue with the spot cleaning but definitely clean the whole thing out once a month, disinfect everything and add new bedding.