We have noticed that especially during peak hours it seems that TM throttles / traffic shapes FTP connections. Those on seedboxes may experience slower FTP transfer speeds that necessitates using many threads.
We have found that passing the FTP program through theVPN massively increases this speed.
Without VPN: 4.3 kB/sec
With VPN: 100 + kB/sec
This was all done on ONE thread on the same server. Something worth exploring should you be hammering your head on why FTP speeds are less than spectacular.