I have exactly the same issue here with my FaderPort 16 (3.44, 17431) under StudioOne 5 (datareduction 0%)
left: working state, right: broken state
I contacted the Presonus Support they told me that I should send it in for repair.
From another source I heard that they work on the firmware...
What's true ?!
The only workaround, after which anything works as expected, is to powercycle the unit until it works, sometimes it is just one on/of, another day I have to turn it on/off multiple times eg 6 !