SurferTim:
There has been a problem bricking the usb chip if you supply power to the +5v bus without disconnecting the +5v bus from the usb power bus. I do not know if that was your problem since you have a custom board.
I have noticed that our Mega board is a little picky about the order I connect the power and the usb cable. (But I thought all Arduinos are picky about this?) Is this a somekind of latch up problem. I think I'll cut the usb + power trace.
Edit: tried to make the meaning a little clearer in (But I thought all Arduinos are picky about this?).