Hi , could you be losing CO2 in your filter? If you pressurise the canister(assuming it is a canister filter) the CO2 could find a way round seals.
When you had the diffuser opposite the inflow did you still have the high bubble rate?
Not something I thought about but the gas entering the filter isn't under pressure, the twinstar diffuser is sat under the intake in theory the filter should just act as another diffuser and distribute the CO2