Ah, I missed the \Data\ folder. Hopefully people will notice like you did, thanks for pointing that out, it might help if someone can't get it to work and made that mistake.
I too noticed the level 2 attribute not sticking, so I just applied it proactively in the .lsx, added 1 point where I wanted. My henchmen since have been getting all the usual level ups, so maybe it's just that one that doesn't work for some reason.
Glad it helped you.
