When logged in directly to the OBi (at the IP address reported when you dial ***1), MessageWaiting is not listed under SP1 Service -> Calling Features??? I'm running a somewhat old 1.3.0 (Build: 2586), but it's hard to believe that this was removed from the latest firmware.
Also, under Physical Interfaces -> PHONE Port, try turning off MWIEnable and VMWIEnable.
If no luck, one option would be doing a factory reset and reloading the config. Another would be to change Tone Profile A, so that Stutter Tone was the same as regular Dial Tone.