Yes, it seems that power management always on definitely fixes the issue. We were worried about the internal temp of our machine, but it seems to be negligible enough that we are going to proceed with using this setting.
Yes, it definitely seems like the issue is a slow turn of the enable signal. I was under the impression that changing the jumper on the V9 from 3.3V to 5V meant that it would output 5V logic. Is that a wrong assumption?