Skippy Skipping?

We're not quite sure what the deal is. Our Skippy filter isn't living up to what everyone has broadcast. Granted, we've had ups and downs of late with our pumps and such, but we only had clear water during the baby shower in June - right after installing the filter - and it's been green since a few days after that.

Steve couldn't help himself: he just HAD to take out all the scrubbies and rinse them out and put them back in. He's even taken out the plants. (argh) We've done a few water changes / pond flushes, and still the water is green. What the heck, man?! The fish don't care, but WE WANT TO SEE CLEAR WATER!!!

PS: Replacement pumps still not received from Beckett We've removed the Y and are just running the 3500 gph pump through the filter.