Something else no one brought up, is that there is a bacteria called coccidea that is naturally present in the gut of bearded dragons. Usually, the dragon's immune system keeps the population of bacteria in check and is never a problem. However, bearded dragons that are immunodeficient for whatever reason, sickness, poor husbandry, poor diet, etc, can have flare-ups of this bacteria and a smelly stool is one symptom of this.
If you clean regularly and still encounter this smell, I would take the dragon to a herp vet and have a fecal analysis done, with a specific test of the level of coccidea present.
If you clean regularly and still encounter this smell, I would take the dragon to a herp vet and have a fecal analysis done, with a specific test of the level of coccidea present.