Hello Georg, you may be quite right about what makes sense in this case. I did suspect that some particles in the developer might cause the problem, so before I run the last film in the old developer I filtered it and did find at the bottom of the filter some needle shaped crystals, but not shaped in anything like the "flakes". Using that filtered developer still ended in a lot of "flakes" on the film. I agree outdated developer shouldn't cause this to the emulsion, that's why I suspected that it might be some contamination due to not sufficiently cleaned equipment.

But after all I'm in fact NOT really happy this morning!! After careful inspecting my last two sheet when completely dry, processed with the newly mixed chemicals, I found 2 small "flakes" on one sheet, and 3 small and 1 quite large on the other!
I have now followed your advice and changed to to plastic bottles and filtered the chemistry.
Though we are supposed to have very good water supply in the area, I will probably use distilled water next time I mix the C-41 stuff.