A bit late to the party, but I'll add:
I clean the liner of my helmet frequently, and always wear a liner that is regularly laundered.
For me the itch sensation is caused by my hair being pressed down in a direction which is not normal. It only happens once in a while and I've gotten better at avoiding it. Upon removal of my helmet and liner, my scalp shows very unusual cowlicks and part-lines on it whenever the itch shows up.
If my scalp gets itchy, I have to stop and remove my helmet and liner, comb my hair back to it's natural lay, let it relax for ~10 minutes, then I carefully reposition my liner to not reorient the hairs, and reinstall the helmet. If I jostle around my helmet too much while getting it positioned on my head, or if it starts to itch while riding and I push the helmet around trying to satisfy the itch, the liner moves slightly and amplifies the pull of my hair in un-natural directions.