Does any vendor make a network configuration diagnostic tool that would let you run the application at two endpoints, pass data between the two copies of of the application, then diagnose problems with the network settings at either end point? For example, such an application might notice that you have jumbo frames enabled on gigE, but that the TCP Window size is set for a number that is smaller than your jumbo frames (thereby undoing the value of the jumbo frames). The application might notice that you have jumbo frames enabled correctly at the sending side, but that the receiver is getting fragmented packets, indicating that something between the two points is fragmenting them.
Basically I am looking for a tool that will look at things like MTU, MSS, window sizes, unexpected latency, etc and then help to deduce and explain specific network configuration errors or topology problems. It is an extreme drag to have to diagnose problems with things like MTU, MSS, jumbo frames, manually, through knowledge, using of pings, network sniffers, etc. I have to believe that a lot of this could be automated by an appropriately smart diagnostic application.