I had the same issue kinda... I was trying to use an 8" vortex fan on 2 6" x 24" carbon filters.. I took off 1 filter and things cleared up completely... Try breaking it off into 2... It could be either your not pulling enough air, or your pulling too much.... I'm thinking 3-6" filters is too much, and its not pulling enough or you have leaks... I use that aluminum duct tape on everything... even where the pipe is seemed (regular hard/round pipe that snaps together), if you can hear any kind of whistling when the fans running... you got leaks...
Either that or your filters are worn out... They eventually do need replacement... Check the manufacturers website, they will be able to tell you the proper specs on how exactly how much cfm you need to get the proper level of scrubbing...