Hey guys I'm having a bit of a problem with my XT660R and I can't seem to get to the bottom of it.

My engine management light is on and fault code 46 has shown. I'm aware that this is voltage problem and the usual suspect is a duff battery or the charging system.
I've checked the battery (it's a new one) and I'm getting good voltage with yhe multi-meter. I've started the bike and the voltage increases to around 14.5 as the revs rise, the stator reads correct voltage, connector to reg/rec is good ect. So charging system is fine.

When I go into the CO menu to see the Rev counter and start the bike, it runs fine. Then if I turn the ignition off and on again the light clears and the bike starts and runs fine, before inevitably showing the fault code again, even whilst I'm riding?

I've also checked the battery's voltage through the diagnostics menu and it'll usually show 7-9 volts.

I'm not really sure where to go from here?

That reading is far from normal? It should be, give or take a few tenths of a volt, identical to the battery voltage. Minimum of 12V, and more likely around the 12.5V mark with a new battery.

If you know the battery is good and is giving you ~12.5V at rest, the charging system is delivering 14-14.4V with the engine running and you're getting just 7V in diagnostic screen, then the first thing to check would be all the associated connectors in the FI/ignition system for corrosion, poor contact and high resistance. A poor connection can/will cause a significant voltage drop in the circuit with which it is associated.

Check all connectors in the FI system, including at the ECU. Also check the connections between the battery and the ignition switch, the main switch and fuse (check the fuse is seated properly and the pins are clean too), at the injection relay and the connectors between the engine stop switch and the FI relay. While you're at it check for abraded wiring and/or short circuits.

__________________