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Chill filtering is a bit like liposuction—it removes fats and usually isn’t undertaken for health but for cosmetic reasons. Chill filtration is a technical process, executed before bottling, that distillers use to ensure that their spirits stay crystal clear on your shelf.

The short question - is there a better filtering method than double coffee filters?

The longer explanation -
I recently decanted two new oak casks of corn/rye whiskey. Cask (A) was clear and Cask (B) was cloudy. Both casks had been rinsed and naturally sealed by holding water until they stopped leaking. The source liquor was the same, casked at 125 and they were stored identically, so obviously something in cask B caused the cloudiness. I assumed that some sloughing of some kind must have occurred of the wood (cellulose particles?) inside cask B so I ran it through a double coffee filter. This had very little, if any, effect. I put it in the freezer to see if it might settle - nope. The cloudiness is very evenly distributed but if I leave it for a week or so small "cluster clouds" appear - looking like floating dust-bunnies - as the the particles group together but they don't settle. Any ideas on how to filter this better (for appearance) and any idea what it might be?

If it's 125 proof it's not fatty acids causing it. Fats will stay in solution above 92 proof and you won't see cloudiness. As for better filtering I don't know of a simpler solution than what you did. Everything else is going to be more expensive and complicated.

No idea, as I never aged anything in wood.
But filtering again after the clustering might help?
I did a test with several protein sources like skimmed milk, isingglass or egg white. Not easy or straightforward, but might help.

Your liver should clear all that cloudyness up for ya.

Yeah. But it may take revenge for its heavy task.