I know what you are going thru, using Max 2015 SP3 I couldn’t get my multiple UVW channels to stick either, was also using editable poly. I would flatten/position channel 1, collapse stack and add another UVWUnwrap mod for the 2nd channel, rinse/repeat. It refused to save the 2nd channel, I even went to the Autodesk forums to make sure I was doing it correctly (maybe I was missing something new). Even after a mod at Autodesk explained the exact same process I was doing, it still didn’t work!
What worked for me finally was, instead of collapsing the stack, I stayed in the editor and positioned all of the channels at once, then collapsed… it worked. It was extremely frustrating and it shouldn’t have been. After reading your post about this, it has to be a bug. I have Max 2016 now, so I’ll have to test to see if it still does this. I’ll try editable mesh option also.