I had the same noise on my 99 Magnum 500. After lots of searching, I pinpointed the noise to worn front A-arm bushings. The bushings were NOT wasted, but were worn just enough that the A-arm would slide back and forth a small amount. The noise only ocurred from a dead stop. It also sounded like it was originally in the rear of the machine but turned out to be the front. Also, if your Scrambler is a 4x4, then check the slip joint in the front drive shaft and the U-joints. The slip joint is a very good spot to have wear and can be checked simply by twisting the shaft back and forth. Hope this helps!

 

My Xplorer does that every now and again. Usually means that I need to tighten the chain. On mine, it is the sound of the master link whacking the chain guard which seems to stop after I tighten the chain.