So just downloaded and installed 9.0.6 (upgrading from 9.0.4).
I am still having the issue that custom design rules are not being applied, unless I move/ rotate the footprint.
Prior to rotation:
After Rotation:
I have a custom rule that only applies within a courtyard, where the clearance between LVDS signals can be less that normal to allow for routing.
I cant seem to find the topic, but I am sure this was something that was to be fixed in 9.0.6.

