When I break on my 00 SM500 I dont have a trouble stoping but there is a distinct sound coming from the back end. It kinds sounds like a chain comming off of a sproket. I brought it into the dealer the definite heard it but could not find it. They claimed they pulled it all apart and such but it did not go away. I have put 200 miles on it with out any failure, how ever try selling a machine that sounds like that. They did say they would warranty it for 1 year since it was noted. That just does not sit well with me thinking that I will be broke down 50 miles from bumb f#ck ya know! So if you know any ideas or such let me know. I would appricieat it.

 

You might want to try tightening the chain up a bit, the Polaris Trailboss 250 we have had the same problem because the way the back brake works [the chain actually stops when you hit the brake and it stops the back end] so if the chain was loose the slack would finally catch so it would make a loud clunking noise.
I hope you can make sense of that but its hard to explain.
I would try tightening the chain first off.

 

I have shaft drive.

 

Be sure the brake disk and caliper are tight.
Also, check the rear hub nuts (the ones that hold the rear hub onto the axle). I had a hub work a little loose once and it will make a popping or creaking sound under certain conditions. Kind of a POP, POP, POP sound sometimes, and sometimes just one POP. If it goes POP when you take off also, it is likely the hub popping agains the axle. Just be sure they are tight. I doubt you will be able to overtighten them unless you have a 2 foot long wrench.

 

My Brand new Sportssman 400 has the same noise and so did the demo I rode, I,m pretty sure it is the spacer put in the rear caliper to keep the rotor from getting damaged when the brake pads wear low. It is only held in with a single clip pin and if you abruptly role the bike back and forth a few inches even with the engine off it will rattle. Hope that helps!