Log into the OBi at the IP address returned by dialing ***1. You cannot do this from the OBi Web Portal as the needed setting does not exist there.
Disable Auto Provisioning and reboot.
Go to:
Voice Services -> SP1 Service -> MessageWaiting
and uncheck the Default checkbox and click Submit. Unplug the power from the OBi. With the OBi powered off, clear the Message Waiting Indicator on the phone. If the Message Waiting Indicator on the phone returns with the OBi powered off, the problem obviously isn't with the OBi. Plug the OBi back into power and go back to:
Voice Services -> SP1 Service -> MessageWaiting
If the checkbox immediately to the right of this setting becomes checked and your phone again reports Message Waiting, it's the OBi that's turning it on. If the checkbox stays unchecked, the phone should not turn on its Message Waiting indicator.