I see there has been three update requests filed. I'm going to go on record as saying after the big patch I did not having any problems using any options in the trainer. I'm using GOG version.
I have taken to editing attributes through CoSMOS at character creation now that I can extract and edit the game files directly to change the caps and various other things though.
Likewise, no issues with the trainer since the update was filed. I too have been directly editing the attributes via CE.