I tested it a bit more and it seems any progression that is above 1:0 has this problem. I understand how this would be tricky to fix, and it is not going to keep me from using the machine, but it seems quite a big limitation to only be able to use the progression feature on 16 steps.
All my patterns default to 32 steps so I expect all 32 steps to be played through when I adjust the progression. I love this feature, but I would probably not be able to use it live because I would have to think about which section I am on when I adjust the progression, and it is more difficult to predict the outcome, so more dangerous for performance. Too many variables to track.