There are two (for want of a better word) modes in which to transfer – or, two STRUCTures. Record or File mode.
on the iSeries, start an FTP session, and run the command STRUCT without any parms. This reports back the current setting.
I would try to flip the mode and see if this helped
So, if currently in File more, you can STRUCT R to flip it, or if currently in record mode, then a STRUCT F might help.
Not sure if this would help, but it is a starting point.