Read "Most Common Problems with the Raptor 660", a sticky at top of the General 660 Discussion section - pay attention to the RPM limiter section, as Willy has suggested. Does this sound like your problem?
'01 660 Raptor, Burgard +2+1 arms, YFZ Shocks, LSR anti-vibe, CTR pipe, jetted, K&N
'01 Polaris Scrambler 400, K&N
'02 Honda 400ex, Big Gun pipe, jetted, K&N, Lonestar +2 A-arms, Lonestar anti-vibe
'02 Honda 400ex, DiamondJ +3 A-arm widener, Lonestar anti-vibe