I had the same problem and it turned out to be the mic stand touching part of the floor tom. They were cheap stands and it caused a very loud rattle on the recording. Only the mic for that tom picked it up too. I would start with checking your stand for rattles. I will post a quick clip if I have the chance.

The thing is...I'm not using stands. I'm using clamps on the drums themselves.

Have you tried using tape? Or maybe those rings that you get for drum heads? They always worked for me. Make sure it's not the drum itself.
Good luck

Take the mic off and hit the drum, if you can hear the rattle there and it isn't the mic causing it, then a lug or peice of mounting hardware is loose. Take the drum off and take one of the heads off and tighten all of the screws for the lugs inside and for the clamps etc etc.

And if that doesn't work, try drinking heavily, and yelling cursewords at the drum. (F*c!n piz'a she*t)
Sometimes throwing it across the room helps too.
2 or 3 times :lol:
It will at least "change" the sound :roll: