Hmm. So with the hotbox setup I have. I can align my manipulator to an edge, switch to another component (face/vertex/etc) and then select "custom axis" to go back to the manipulator I saved. With this, it seems to "forget" when I go to custom axis.
Alright I think I got it working again for 2015 and 2016. Let me know if there are any issues. If in Edge, Face, or Multi mode, the script will look at what's pre-selected and set your manipulator to that edge's axis (or face normal). Running the script while nothing is pre-selected will reset the axis orientation settings…