For future reference on this topic, there's a field under each SPx service in an Obi -- SPx > Calling Features > MessageWaiting -- that is 'read only' (meaning you can not change it, the Obi logic changes it) and it will tell you what the Obi thinks is the correct Message Waiting state.
This is independent of the analog phone handset you are using. So if it's on and no indicator on your phone, suspect the phone or settings. If it's off and there are unread messages in GV (or any other provider) something is suspect in the Obi getting interface to the service provider.
I was going to ask someone to elaborate on what new version of the firmware you are talking about, but I now see "3.0.0(3722) for OBi202/OBi302" listed under as updated today, Jan 24.