I'm sitting here at work and I don't have access to the official WoW site to check but I was hoping that maybe someone could tell me if they've fixed this issue? It's been a major PITA the last two weeks.
I can't say for sure this is the issue you are having, but the new CTMOD/CTRA has had numerous conflicts, one of which is effectivly breaking the windstones. Try turning these addons off before retrying and see if it helps. The other issues i know about with CT include problems with argent dawn commision working, and pet command bars not appearing in combat.