Most disinfectants are designed to work on clean surfaces. If there is a lot of 'gunk' (mucous, saliva) stuck in nooks and crannies it cannot penetrate to do it's job. You think your doing a good thing, but you aren't really doing a whole lot. Clean well first (at least rinse well), then disinfect.
The 2nd stage has a lot of edges and places for saliva to collect. A simple dunk doesn't do a very good rinse job. Use a semi-clear mouthpiece for a year and you'll see growth + discoloration on it, usually serratia and some other fungi. You won't see it with a black mouthpiece, but it's still there. Same inside the reg.
Occasionally you should open the reg up, spray simple green or such into it, then go at it with a soft toothbrush. Remove the mouthpiece and do the same thing. Then soak in your disinfectant of choice. I just use 50:50 vinegar:water for 10-30 minutes. It works well for these kind of organisms.