SystemConsole (on its own) gives you access to the target system but will not immediately tell you what's going wrong. If you put a JTAG Avalon master in your system then you will be able to read and write through it to get access to slaves connected to it.
Whether this is useful depends on which slaves you have connected. You may be able to access registers in the Ethernet macs which give you more information. Alternatively you could write a simple debug slave and use that to return information about what is happening.
Or you could use the transceiver toolkit to check how your interface logic is set up, but if you can transmit 1:1 then that is at least partially working.
I wonder whether your problem is lower level than that though. If I remember right then switched Ethernet sends flow control frames in the opposite direction to the data. Without these frames the transmitter won't send anything.
If your connection cable does not connect the tx pins from the receiving board to the rx pins on the transmitting board then the flow control won't get through. Alternatively if it connects multiple sets of tx pins on all the receiving boards to the transmitting board's rx pins then the different tx pins will interfere with each other.
Could you use SignalTap with suitable triggers to record what is happening on the rx pins of the transmit board?