I've got the same problems with the Kenny boss fight and the four perks never unlocking.
It probably is a combination of using the trainer and the game being buggy.
I mean when was the last time Obsidian released a game without any major bugs.
I going to try using CoSMOS to see if that still causes problems. If problems persist, I'd say it is definitely the game.
[Edited by Bardorp, 3/10/2014 10:45:35 AM]
regarding the perk points, all the trainer does is write to ONE address the amount of points. if you add more than 10 it sets it back to 0. If there is some mechanic in the game code that detects how many points you have USED already, our trainer doesn't have any ability to mitigate that. it just gives you 1 more point each press, and resets to 0 if you add more than 10.
best,
Cal