Doesn't sound like there's anything wrong with the filter--live algae clogs up a DE filter in a hurry. The only way to clean up the swamp is lots and lots of chlorine--but if you can't bypass your filter, I don't know what other option you have other than to babysit it. You might be able to add a shock dose of chlorine and keep the filter on long enough to circulate it, then turn the filter off and let the chlorine work, but I'm not sure how effective that would be. Hopefully some of the other DE filter users around the forum can stop by shortly to offer some better suggestions.