From your description it sounds as if the media tank is not backwashing properly and the media is loading up and restricting flow.
The system you have injects air as an oxidizing agent and presumably to meet the oxygen requirements for birm to work (the tank with the pump on top) and then filters the water through birm media. Here is a link describing birm media and the conditions necessary for it to work properly: http://www.caitechnologies.com/image...specs/birm.pdf. If you in fact have hydrogen sulfide that may be the problem--birm does not work with hydrogen sulfide present.
Here is a link to the manual for your system and I recomend you read it if you have not.