this may be a stupid question but have you checked to make sure your skill requirement is high enough? as in you may have 59 in archery and you may need 60?
sorry if thats too obvious its just i've made that mistake once or twice myself. i was planning an upgrade but did'nt have enough points so thought i'll get it next time, then forgot how much i needed to get it and when my skill was increasing i thought cool i've got enough now. then when it came to level up time i went straight to the perk i wanted and was like whats going on, why can't i get this, all because i forgot to look at the skill requirement again. it's easily done.
if not that then maybe another glitch because as far as i am aware you can reshape your character at anytime you want so all skills should always be open to you provided you have the required skill level.
hope you get it sorted cause that would be really annoying. let us know if you figure it out
