I'm having an issue when cutting lexan/other higher machinability plastics.  Right at the end of cutting a part, the waterjet will travel over the material before the jet/abrasive has shut off.  It only does it randomly and not on every part.  And even with just a few seconds on the plastics they're marked up and no good.  Any ideas please???

May be you can set it on control system.What system control your water jet cutting machine?

It sounds like an actuator issue or your "water off" delay timer is set a bit short not allowing the cutting head enough time to fully shut down. We use mostly Jet Edge Omnijet heads, I find this particular problem typically happens when the breather filters get old/clogged and slows the actuation time down, its a common misdiagnosis among the operators.