As said above by Jantex,
Waterbased emulsions are (in my opinion) far more susceptible to being locked into the screen by other chemicals.
Can you tell us what kind of waterbased inks you're using, any screen openers or screen cleaners that you are using on the inks as well would be helpful.
Another thing I always ask people when it's emulsion issues, is this a NEW issue, or a problem you've been having for a while? Any emulsion that has to be sensitized (Diazo Emulsions) have a shelf life once mixed. It's usually 1-2 months depending (some go longer), but obviously you'll start to have problems with screens as you get to the end of the shelf life on it.
Lastly, you said you're having problems removing emulsion after it's been burned. So is this when you're trying to rinse out your image, or you are trying to reclaim the screen?