PhotoEngineer has commented on the chemical properties of stabilizer several times, and from what I read it doesn't contain any critical chemicals which could possibly produce those flakes.
One thing did come to my mind, though: before you stabilize, you perform an extensive wash. Could it be that the wash introduces these flakes somehow? I could imagine that the flakes build up in the stabilizer only as some of the flakes introduced during the wash end up there. And since the stabilizer is the last step, film after film it is less and less able to wash away these flakes as it accumulates more and more of them itself.
Just my 2 euro cents ...