Full Duplex vs Full Duplex w/flow control?

take a look at your switch, some times auto nagocate can fail and cause issues, if you set up both ends manually things might improve.

TCP/IP has its own flow control mechanisms built in which is somewhat more sophisticated than ethernet flow control. This is especially true on busy switches with multiple links to hosts at different speeds - TCP's connection-based flow control is better than ethernet's port-based controls since one slow port on the switch won't necessarily impact other clients.

To explain that a little more, consider the (simplified) example where you have one server connected to a switch at 1gbps. On the same switch are 10 other hosts connected at 100mbps and one poor soul on 10mpbs.
All client initiate a transfer to the server. Pretty quickly that 10mpbs host maxes out its connection and starts emitting ethernet pause frames (as part of the ethernet flow control). That pause frame is passed back to the server which now pauses transmitting.
Since the pause applies to the entire ethernet connection and not just the TCP session between the server and the slow host, ALL the traffic from the server pauses, causing all the traffic to the other hosts (which have ample bandwidth available) to also stall.

That's why TCP's flow control is better than ethernet's - only the particular streams between server and (slow) client will slow down, leaving everyone else to continue at their respective maximums.

As such I always turn off flow control unless your network traffic is primarily some other protocol that doesn't have its own mechanism (e.g. UDP, broadcast or multicast)