Sounds like a loose headset. The clank you hear is the bearings hitting the race. I would check for a loose headset and make sure if you are using a threadless style fork, that your bolts are sufficiently tight and there is no grease on the steerer tube. Both can lead to slipage and can cause the clank you mention.

I more often encounter this on carbon steer tube installs....

It won't go away on its own, its an adjustment issue

I just re-read your post, and it goes away with another set of wheels? I still think its the HS. Perhaps the set it does not occur on is tensioned looser with more give.....