Further information. The board occasionally hangs and won't reboot with a power cycle. The only way to start the system at this point is to hold the "power" button on the T1040 in until it is started. Don't have a real idea of how long this is.
If the system is powered off for a minute, we get into this situation.
Don't know the revision of the board as it is in a remote office and there is currently nobody there who can check it. Can this be determined via u-boot?
At the moment we are thinking excess startup power draw on the PCIe bus... I will post more as more information is obtained. It may be a few days.