uploading, aborting and resuming uploads creates corrupted files on some servers. WinSCP uses the APPE command to resume, FileZilla uses REST+STOR.
Some time ago FileZilla also creates corrupted uploads, but this is fixed now.
Use REST+STOR to resume upload instead of APPE if server advertises REST STREAM support
Is there a chance that WinSCP supports the REST+STOR command if advertised by the server too?