Just tried an experiment. I made sure I had enough power points to fill all the boxes. I then saved the game. I went back into the game without the trainer and powered up all the points. With no trainer, it seems to keep the points. However, when I went back into the game, with or without the trainer on...the powers were lost.
This is a serious bug guys. I am noticing now that it clears all the points even during the game, like when you leave the Normandy or go into a side mission.
I have tried the method you recommended and it doesn't work.