On-Board connection of ethernet transceivers
You may have some trouble if you don't provide a resistive padding network between the two ports when you cross tie them, to simulate the damping you'd normally get with a length of cable / transmission line, and provide enough attenuation to avoid saturating the magnetics. I have not done this with 1000 speeds but I can tell you of several occasions where I've cross connected two 100-Base-T ports, and found that anything less than about 1/2 meter of cable produced unreliable results. 1000-Base-T will surely be even more problematic. To cross connect them "on-board", you will likely have to have "T" pads pon each leg of each differential pair, and at that speed will have to be mindful of the transmission line characteristics of your PC traces. Now all this is worst case! Depending on the magnetics and filtering already on board to interface to the outside world, you may get lucky, or you may find that one resistor on each leg will do (though you'll still need to be careful of your trace layout!). Finally, if you are scratch laying out a board here, you will likely find that the manufacturer of the transceiver has guidelines for simpler direct coupling, when done before the "outside world" interface. There's a little black magic here sometimes, so I'll end by wishing you luck.