Flake Material in ID after swiss style machining

[bikerbear]

Cutting swiss style .125 DIA 316L SS as well as 304 SS with cutting oil, drilling operations first then Bore or Reamer operation for finished ID. After passivation or a cleaning process, foreign material can be seen in the ID under magnification about 20x. Drills are HSS Ti-n coated, Bore and Reamers are carbide. A team of us cannot figure it out. Metallurgical analysis isn't conclusive as to what it is. Temperature studies have not shown anything, different machines, different parts, different ID, different material heat lots, tool life has been mixed-no canaries in the coal mine per say. Does anyone have experience with this, offer advice for solving this problem?
The flake material can be removed but only if we add another cleaning operation.

Thanks