there shouldn't be any limit... do you correctly apply data trickling to the FTP download? Probably data trickling is not executed, in this case the connection to the FTP server could time out.
do you have a link for me? :-)
I want to test it and can give you feedback.
I think we isolated the problem - when users download via FTP, the malware scanning engine kicks in. We placed a "SKIP SCANNING when protocol is FTP" and all is working now. I'm sure its not best practice but to get my users up and running , we had no choice.