For what it's worth, on my previous boat I noticed red "flakes" in the fuel filter that I traced back to the plastic gas cans I was using. From then on, I would just fill up at the pump instead of transfer. Might those be the type of flakes you are seeing? IF it's getting past the filter, I would say the lines themselves are suspect and due for replacement.
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Walt B
"Debt-Charged"Black '07 H210SS6.2L Bravo One turning a 21P HIFive
Wakeboard Tower with Perfect Pass Stargazer version
Missouri River; Kansas City, Mo.