I haven’t come across this before but I’d be interested to see what files have actually been captured by this process. Can you add a branch with a send to Folder, between the file capture and send to FTP plug in?
You can then compare the file in that folder to the source file and what ends up on the FTP site. If the file in the folder is corrupt or otherwise non functional we can rule out the file capture process. otherwise if the file in the folder is correct and the file on the FTP is failing then we can take a closer look at the FTP output plug in.