I have had this problem.

It sounds like glycerin, or glycerides, coming out of solution in homemade bio diesel. It is often black and insoluble and gets stuck in the primary filter.

I have also seen algae from the tank dissolving in the bio diesel. It takes a while to totally dissolve.

I have about 50,000 miles of B100 experience, but I can't get it any more so I am back to dino for now.

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1991 350SD (updated rods)
Biodiesel B100 when I can find it.
Dino when really cold outside