I haven't seen the engine light outside of power on self-test.
"The warning light turns on flashing to warn about a critical emission-related error that could damage the catalytic converter. If possible, have the vehicle be taken to a Ducati authorised service centre and the malfunction eliminated and at any rate proceed slowly, avoid harsh acceleration and overtaking."
Did you or your dealer check on board diagnostic codes? Sounds like it may be an issue with the O2 sensor or the sensor wiring. I wouldn't expect a firmware update to resolve this behaviour unless the firmware were flaky or marginal, but your experience seems uncommon so I doubt that's the issue. Does anyone know if Ducati has publically available change logs for these updates?