I've been having this same issue with CopperLan 1.1 on Mac. I setup CopperLan, enable all my midi ports and everything works. When I reboot, either all of the midi ports have been disabled, or sometimes one or two ports will be enabled, but all the others disabled. Which ports are enabled and disabled changes randomly with each reboot.
I have installed CopperLan 1.1 a few times and it's made no difference. In the end, I tried 1.0, and that seems to be working correctly now.
I'm on a 2010 Macbook Pro running OSX 10.8.2, and my midi interface is an emagic AMT8.