Ok. I found it. Lol. TONS of posts in that thing so I'm gonna re-post Cals post here so others can find it easier than flipping through 20 pages. D:
Quoted from Caliber:
For those who say that their Level Up Progress Points go away AND their powers reset after saves or moving to new locations, the game seems to do an internal 'check' of itself if you are a lower level than your points distributed say you should be. To correct this, 1) you will need to make yourself a very HIGH level (perhaps level 50, 60, or maybe even 100) 2) distribute your points or auto-upgrade and it will fill all the bars 3) save the game immediately 4) reload and you will see that they 'stick' 5) if you level back to a lower level, the game will readjust your points and may take back some of your powers or reset them all.
I tested this and it works.
All times are (GMT -08:00) Pacific Time (US & Canada). Current time is 11:08:46 AM