I cannot tell from your 4th paragraph if you are crossing over or not.
Automatic crossover detection is part of the IEEE 802.3-2008 or IEEE 802.3ab 1000Base-T spec which uses all 4 pair. You don't have that so you do not get Automatic MDI/MDI-X. Make sure you terminate your orange and green for crossover as explained on wikipedia http://en.wikipedia.org/wiki/Ethernet_crossover_cable.