I've successfully upgraded my skills and ability points to the desired stage however, I am unable to assign the "active/sustain" abilities to either the xbox360 (X,Y,B,A) controller or the keyboard (# 1-0).
The option "Map Ability to UI" (via xbo360 contoller) or "Drag and drop" (for keyboard and mouse) options are completely grey-ed out.
However, if you are played the game from scratch / beginning without using the trainer, it seems to work.
I'm wondering does anyone here face the same issue / bug?
I know this probably isn't helpful, but I'm using a 360 controller as well and mine works fine. It is a corded controller, as opposed to wireless, but I'm not sure if that makes any difference, since you're having trouble with mapping to the keyboard as well.
I'm using the Origin (digital download) version of the game. You could try "Check for Updates" in Origin. It automatically repairs files, etc. when you do. Other than that, I'm stumped.