Well, I'm a debutant here, at the story board as well as on the forum.
This is no complaint, but out of roughly 7,000 readers only 3 took the time to post a review on my story -- well, you're probably familiar with the general quota... And while I appreciate any kind of feedback, it was – so far – pretty much a plain 'good job, keep up the nice work' (which is, mind you, lucky and encouraging enough, I think).
So for me, it's a dictate of politeness to reply with a plain thank you, if only to show the reviewer that his/her remarks have been noticed and are appreciated. Given the 'manageable' number of reviews, even on the most popular stories, this doesn't cost the author any considerable time, and it might encourage others to post a brief review, too, at least. However, any further exchange of opinions should be made via e-mail, IMO, not via reviews and replies.
Still, let me use this occasion to state that I'd have no aversion to say 'thank you' a little more often;-) And I'm always interested in any details which led to an (un)favourable verdict on the story.