The only time I've ever had this problem is when my developer has become full of tar (i.e. it is very oxidised).
If I'm desperate, I skim the black specs of the top of the tank using a paper towel before topping up with fresh developer. This reduces the problem, but I still get an occasional spot.
The only certain cure that I've found is to dump the chemistry. I routinely remove the tar at this stage (using Nova's tar-buster product).
If you have only changed the chemistry, it is possible that the tar deposits at the bottom and sides of the tank have become disturbed and are contaminating the new chemistry.