I did some experimenting and figured out I can reliably trigger RUD when coming out of warp using PR with these settings:
Reference set to anything EXCEPT "none"
Rotation mode NOT active ("rotation" at the top is red, button at the bottom says "activate") SAS on standard stability assist (prograde and retrograde seem to work as intended)
It seems to me that the "deactivate/activate" button is unnecessary and perhaps misleading. Having rotation mode deactivated is the same as setting the reference to "none", and PR itself is always active so the button could be confusing to some people.
Hopefully this is helpful. My install is very lightly modded, and all from CKAN. I didn't see anything unusual-looking in the log, but I can provide more information if necessary.