So when i try to learn skill books my skills are not upping. Anyone else having this issue, or did and have a fix for it?

Do you mean the magazines? Magazines only up your skills for a short time. The actual skill books do up your skills permanently, but there are far, far fewer of them than in FO3. Both types are working as they should for me.

no the actual books like tales of a junk.. etc

I am wondering if its like what used to happen if you used to use in FO3 with showracemenu if you use console commands your perks stop working?

Just got it all figured out.. If I used a console command to do anything ie showracemenu I have to exit game before learning books, as they do not learn.

Yeah well using "setav" in particular can interfere with things that add to stats and skills. "ForceAV" is even worse in this regard.