I've been reading a lot about people having this clacking sound in their engine. Some 450's some 250's, some have had it since day 1; some developed it later...
I believe the sound you guys are hearing is coming from the decompressor system. In the pics, notice the #3 item on the 250 (bottom pic) and the #4 item on the 450. This is the decompressor weight (or inertia arm). This is what i believe is making the noise.
As you kick your bike over, the RPM's are low enough that this arm does not overcome it's own inertia and stays in contact with the cam (or actuator connected to the exhaust rocker). This actuates the exhaust rocker to slightly depress, releasing compression and allowing an easy kick.
Once the engine fires, the RPM's of the engine increase and is sufficient for the arm to overcome it's inertia. The arm "swings" out of the way of the cam (or part that actuates the exhaust rocker). This process allows for the decompressor system to be basically "disabled".
Now, what I believe is happening to your bikes: The processes are happening as intended (the bikes are running and starting OK) with one problem. The decompressor weight is not clearing the cam feature or exhaust rocker actuator completely. This problem forces the decompressor weight (inertia arm) to forcefully swing back to it's "low-RPM" position causing the "CLACK".
Take the valve cover off and investigate. I'm willing to bet this is the problem (without being there ofcourse to properly diagnose). Take the plug out, and turn the engine over by hand. You should be able to demonstrate the issue by turning the motor over quick enough. I've solved this issue before by applying a liberal amount of lube in the area where the arm meets the cam feature. Some may have wear in the parts needing replacement. Good luck and get in there with some light to really see what's going on...