It's been awhile but if memory serves .... try turning ON Easy Level Up AND Numpad 8 Mega Skill Points at the menu, then load a MANUAL save. See if that works.
You may have to make another manual save to test it, then leave and do the above when you restart the game again. I seem to recall when I was using Easy Level and Mega Skill points that's how I had to load the game. Also, don't use Continue.
[Edited by Jaks, 10/13/2017 12:22:56 AM]
Thanks! that didn't work, but I ended up figuring it out. The Mega skill point option is fundamentally broken, because it's tied to level. it causes some sort of weird bug when you first use it. (I think I used mine at level 3, hence the level I was stuck at.) No matter what I did, which order i loaded the game/trainer in, or what options i turned on, the result remained the same.. it would revert me to level 3. However when I disabled the mega skill option, my level saved correctly. So my solution has to been to install a mod that gives more skill points per level (you can choose how many more) and just use the easy level up option to push my character up to 35-40.
However, if I use the infinite skill option now, it may save my level at it's current position and work.. I havn't tested that far yet.
If you have unlocked certain character gear with the Skill Point option (ie weapon holster) and your skill points reset the next time you load your save this could happen.
The Skill Point option has to be enabled prior to the loading of a modified save game.