It's not uncommon for some shocks to be a bit more audible than others when it comes to bypass tubes even of the same make. The First Thing I would do is close the tubes all the way so they are completely locked and the tappet cant move. If you still have the clicking sound it may be something else. If it's gone then you know it's just the sound of the tappets opening and closing doing their thing. When Fox first started the development process of the 3.0 external for the Raptor, they were also playing with the idea of a 3.0 Internal bypass. One of the reasons for a 3.0" internal was they were concerned that the sound of the check valves opening and closing on a street truck might deter people, but as it turns out, the externals were really quiet so that worry was taken care of.
Fox's Tappets are made of a very light material and have a design element in the tappet itself to make sure they remain as quiet as they can.
For the op, I really wouldn't stress on it to much. even on small graded roads tappets open and close at a rapid rate.