I've been trying to migrate to WinSCP several times until now, but somehow always had to come back to my former client to handle transfers between my NAS and my laptop.
This time I decided to dig into the issue, and may have found a pattern.
Basically, it seems that the files are transferred correctly as long as I don't change the front/backward kind of transfer.
Started backward => OK
Started frontward => OK
Started frontward, then set to backward sometime during the transfer => corruption
On the attached log, the 1st and 4th transfer were fine. The 2nd and 3rd led to erroneous files.