Sounds like a ground issue to me.
Was it installed professionally and by MECP Installers?
Where is the 4-channel amp grounded? Bare metal or a factory bolt?
Are the RCA's ran down the opposite side of the car to your power wire?
I am not familiar with your amps, so I don't know if they have a track record for producing bad whine or not, but that is always a possibility. I am using Rockford Fosgate in my truck and have no whine.