Well, I found the reason for this issue.
It seems that (possibly after firmware upgrade) under the Shooting Setting (not IQ) menu there is a 35mm FOMAT MODE (on, off, auto) that, if set to AUTO, changes to 35mm as soon as the camera detects a 35mm lens!
I was using Canon TSE lenses and have never had this issue. I discovered it by chance shooting wothout a lens and later checking format in lightroom for Fugi lenses.
I guess you should bear this in mind. The option may be aceptable, but how it appeared in my camera with no further notice isnt.
BTW: I am still unable to recover those raw files to 4:3 format.
Any hint?