Have you tried running the purifier manually? This will give you an idea if the problem is in the purifier or on the program of the EPC
It is believed that the problem you are experiencing is in the setup of the purifier itself and both the purifier and EPC setup may require major modification to operate on MGO. The purifier was originally setup for heavy fuel, most likely IF380, which has a much higher viscosity and requires the oil to be heated before being processed.
If you contact Alpha Laval they will be able to advise you on what components in the bowel and EPC, which could include the disc stack, all seals, other internal components and EPC program modifications, that will have to be changed in order to allow the purifier to operate correctly on MGO. However once the modifications are completed the purifier will have to be dedicated for use on MGO only because it will not function correctly on Heavy Fuel.
Troubleshooting 101 "Don't over think it - K.I.S.S. it"