In the automotive world I would look at an RPM pick-up (Distributor, cam sensor, crank sensor ect ect), can anyone shed any light how the S2R's or any Duc for that matter pick up the rpm signal?
In Magneti Marelli managed Ducati-land, the tach signal sent to the gauge is "filtered" through the ECU. If the ECU had a bad tach signal, the bike would likely exhibit strange running behavior... but it's pretty simple to test. Swap the RPM pick-up with the speedo sensor. If strange gauge behavior switches... there's a problem with the sensor (in my opinion this is highly unlikely).
There are some potential pitfalls in the wiring... check ground wires for resistance/looseness.