I had a similar issue and it worked itself out within a few weeks of grinding. We use our grinder for similar methods plus espresso - my extractions were always consistent tasting, extremely over extracted, extraction time for filter coffees was really long and the coffee bed surface was totally coated in silty fines. I attributed this all to having new SUPER sharp burrs, that, even though calibrated, still created significant fines due to the fact that they were TOO sharp. Don’t know if that’s actually true but would love to know if it is. For whatever reason, this problem leveled out within a few weeks of grinding and the coffees went back to tasting like they should: incredible. My advice would be help us find out if it is indeed fines contribution and why they are created, and also stick it out until you notice an improved difference. Oh, and make sure you’ve calibrated your burrs too–I didn’t have any clumping as you mentioned-just really fine, consistent and fluffy grinds.