Does it "clunk" when out of the boat and you work the drive? If not:
May be the end of a long stroke when the fins slap the hull. You can adjust the pedals so the fins don't slap the hull while pedaling and You can reduce the stroke distance slightly to stop hitting the hull. Your leg should be nearly fully extended when at the end of the stroke.
Be sure the drive is installed correctly:
http://www.hobiecat.com/forums/viewtopic.php?f=60&t=12836 a drive tipped forward will cause the masts to hit the well.
If it clunks when out of the boat it can be a sprocket tooth catching the chain. The chain may have a slight twist.