I'm almost going to guarantee your problem is acoustic feedback from the sub. I know, because I had the exact same problem, and the way you're describing it was exactly how I would describe it. (And my turntable was also on a very stable surface, a granite countertop.) The way to know for sure is if you have another source besides analog (like digital), if the muddiness is there with both, then yes you may need to look into proper EQ for the sub, but if it's only the vinyl, then its feedback.
The solution is simple: get a 12x12 (or 18x18) stone tile from any building materials store, and put four sorbothane feet on the bottom. Put your turntable on top of that. For me, the bass boominess and rumble disappeared immediately. I have a lot of second hand vinyl, and I never see a rumble issue unless the record has serious warpage. Improper setup can also increase rumble. I have no filters in my system, and it plays everything just fine (even with subs) after doing the fix above. Good luck!
The solution is simple: get a 12x12 (or 18x18) stone tile from any building materials store, and put four sorbothane feet on the bottom. Put your turntable on top of that. For me, the bass boominess and rumble disappeared immediately. I have a lot of second hand vinyl, and I never see a rumble issue unless the record has serious warpage. Improper setup can also increase rumble. I have no filters in my system, and it plays everything just fine (even with subs) after doing the fix above. Good luck!