I have had the very same problems with Fomapan 100 in 35mm. It was terrible using Fomadon Excel, and got better when I used liquid developers.
I experienced the same thing with Adox CMS 20 the other day, and mixed up new fixer for the second film I developed. The film processed with fresh fixer was much better, but still had quite a few marks that took ages to clone out after scanning.
I too would be very interested to find a "cure", as marks like that drive me absolutely bonkers.
I never ever ever get these marks with Ilford and Kodak film, only with Foma, Efke and Adox.