Its probably the starter's bendix drive kicking in or out. Once in a while mine makes a loud clunk when it kicks in. But I have heard it before on lots of Harleys old and new so I don't think its anything to be conserned about.
If it really bothers you stop in at the dealer and ask them, odds are they will tell you its normal.
Mopar - what year is your bike??? If it's one of the new 2007 models then this is quite normal and a design feature of the new type compensator/primary setup.