We have two servers in different data centers which are geographically separated by several hundred miles. The RTT (round trip time) for a ping between them is 61ms over our VPN. Both servers are on a gigabit WAN link.
Any type of file copy, whether SMB (drag and drop), FTP (tried FileZilla, TFTP, etc.) is excruciatingly slow, at around 1 Mbps. I've tried enabling and disabling Receive Window Auto-Tuning Level, multithreaded copy, and so forth. Our firewalls have lots of CPU headroom, so VPN encryption doesn't play a factor.
I thought about manually setting the TCP window size because it seems like an obvious candidate here but my understanding is that Windows Server 2008 R2 ignores any custom TcpWindowSize setting in the registry.
Update: TCP Window Sizes appear to be fine. Wireshark shows Window Size 513 with a Window Size Scaling Factor of 256 for a Calculated Window Size of 131328. Does this sound right? Bytes in flight stays at around 9000 bytes during an ongoing FTP transfer.