I think you guys, Athiril and hrst, are on the right track! "Flakes" is the right word pointing to a solution, not "spots" as I used; and, yes, some kind of damage to the emulsion is perhaps the most reasonable suggestion. I have now refixed one sheet and just tried to wash another sheet, they are still wet, so I will wait to see if something has changed.
Assuming that it's some kind of damage to the emulsion, rather than something with the chemicals, I started to think what I did that differed from my earlier very limited C-41 experience (5 rolls 120-film in a ordinary Paterson tank (38/100F) with ordinary agitation each minute, and 4 rolls at 30C/86F, 1 roll 120-film in a Jobo CPE-2 with a 1520 tank at the low rotating speed on the Jobo machine). First this time I used, as recommended by some sites, the faster speed on the Jobo machine; I used a bigger Tank: 2553, and with this new tank I found another method for washing which looked very effective but probably TOO effective, the water flow probably too rough, perhaps the control of even temperature during washing and stabiliser wasn't the best.
Perhaps the "flakes" are not something ON the film surface but rather some pieces of the emulsion that is missing, due to improper treatment. Sounds promising! My recent treated sheets are now quite dry and nothing seems to have happened to the "spots", which confirms my suspicion that it's rather flakes of emulsion that is missing.

I will soon make a new try and be more careful in the later stages of the process, and see if this is the solution!
Now, developing 4x5" sheets and 120-film (negative colour film) with the proper Jobo film holders in a 2500 type Jobo tank, should I use the slow or the fast rotating speed?
Many Thanks for your smart comments!