Yup, Reg, Mike hit the nail on the head: ammonia is a no-no to water-based acrylics, just like Windex which contains the stuff. I use Microscale Micromask which is also water-soluble but seems to be benign on acrylics, provided that they are thoroughly-dried/cured and that you don't handbrush water-based paints (or spray on a heavy wet coat) over it. Sometimes Micromask is difficult to take off, though, as tweety1 said, specially if it's laid on too thinly. In those cases I sometimes dab a piece of sticky tape onto the masked areas and try to lift the Micromask off gently, but most of the time I use a water-soaked cotton bud to dissolve a portion of the mask. Once there's an opening, I peel the mask from there.
Sorry I can't be of much help to your problem, bro. You can try spraying flat clear over it and hope it evens out the shade, you'll lose nothing anyway. By the way, did you apply Future over your acrylic paint before masking?
Cheers,
onyan