Mine made a couple of different "clunking" sounds in the past year. The first one made it sound like I had an old one-piston low-speed engine going the whole time I pedaled. I finally figured it out when one day I couldn't remove the drive! Got under the yak and found the main shaft had come loose and had been slowly working its way back. The clunking was from the shaft bumping the back of the drive well, and it finally moved back far enough it couldn't clear the "shelf" (is that the right term?!

) at the back of the well.
The second noise was lighter / quieter, and I could actually feel a "bump" in the pedals when it happened. Lubricating everything seemed to help for a little while, then it'd start again. Finally noticed the shaft of the idler pulley was sticking out! The setscrew had worked loose and it was working its way forward. That caused the back end of the pulley to move side to side.
I put it all back together and ah, blissful silence! -- For a short while. Then it started doing it again! Looked into things more closely and found that the idler pulley was VERY tight on the shaft, even if I lubricated it. The shaft was turning in the plastic housing. Then the ring the setscrew threads into cracked! Argh. Took the drive back to my dealer and got another one.
I'll admit I didn't attend to maintenance like I should have the first six months I had the drive, I suppose it got well-worn during that time or something. I've been more attentive to the new drive, hopefully it won't get into such a state as the last one!