Finally I think the problem is solved! Something must have happened to my chemistry; no doubt I overreached the 6 weeks which the Tetenal manual says is the durability for used and mixed developer with at least 4-5 weeks; I stored it in brown glass bottles, but the top contained some air and I didn't use some ant-oxidation spray. After some try with this chemistry, changing to the low rotation speed on the Jobo CPE-2, keeping all chemistry and washing water and stabiliser very close to 30°C the result was as disappointing as before.
I don't doubt that the "flakes" came from damage to the emulsion: at the bottom of the thank after stabiliser a lot of flakes glittering in clear cyan and magenta colour, and no doubt at certain spots something was missing in the emulsion with shapes close to flakes!
Mixing a new liter chemistry and running this evening two sheets of Ektar 100, the same procedure, temperature and care as above, the sheets came out nice and clean! Very, very satisfying to say the least!!!
Perhaps the chemistry wasn't just a little bit old, some contamination may perhaps be a better explanation. After all it was just something like a week between my first roll with the Jobo machine, without any problems, and the next developing session that started the "flake" problems. I used tanks and film holders bought second hand on eBay from many different sellers. Perhaps the first lesson is to be very careful with cleaning the stuff before using it; I just used them, they all looked nice and clean, never thought of starting by cleaning everything. Maybe that was the beginning of the problems.
At the moment I'm quite Happy!!