The ISP can definitely throttle FTP traffic potentially, but I think it would be good to check whether you're seeing bits or bytes in the FTP application. Most FTP applications I know of show MegaBytes rather than MegaBits. I'd expect to see 60 megaBytes over a 500 megaBit connection, and around 5 megaBytes over a 40 megaBit connection.

You could check the Windows networking throughput which displays in megabits, in the Performance section of the Task Manager.

The Vigor 3900 is quick enough that it shouldn't cause any throttling until you get near to 1 gigabit throughput, but check that the MTU is set to the correct value for the ISP.