OK, let me clarify a few things:
You've made scenes for movers, right?
You've made scenes for cans, right?
Did you make scenes with movers AND cans?
The DMX Operator Pro, while not the same as my older and far more limited DMX Operator, does not work in a manner where you can overlay things.
First, you make your scenes. You've done this, so we won't go on and on about that. But, did you do the scenes RIGHT for what you want to accomplish in the end? That's the bigger question.
Second, you program your chases, which it also sounds like you've done, so no need to get into that either. But, if you haven't done your scenes right, then naturally, your chases won't come out right either.
I think you're not programming your scenes correctly, and that's why you're having these sort of issues. There is to the best of my knowledge(because I don't have time to download and read the manual as I'm quite ill right now), to do any sort of syncronization of left/right side stuff. I could easily see having your movers doing their thing and then you manually manipulating the right side to tweak the 8 channels of cans if you should so desire to do so.
Let me know if this was of any help.