I have to say putting a waveform monitor in our flypack was one of the best things that I have ever done. We did a gig a couple of weeks ago and I was able to look at the scope and see what the problem was between the two cameras and I was able to adjust and make a bad situation not quite so bad
I would try feeding a test pattern from the switcher to the projectors and adjusting to make sure everything is right. If it still doesn't look good start eliminating components till the problem is found.