The problem might be caused by the fact that the LAN port is waking the system. Please do the same checks you did for this PCI Express* LAN Controller, on the onboard LAN port, and ensure that all "Wake on" options are disabled in the Device Manager.
Also, check the BIOS, (In later Intel(R) desktop boards you can enter the BIOS setup program by repeatedly pressing the <F2> key during the boot process), under the Power Tab, and ensure that Wake on LAN from S4/S5 is disabled.
Sorry, thought I'd mentioned that... I did disable the Wake on LAN in the CMOS setup screen, exactly as you prescribe, with no benefit. I didn't try changing the Device Manager wake settings for the onboard port. I'll try it in the morning.
Okay, here's an update. I have another system with the same mainboard, a "virgin" machine that has never had either of my PCIe test boards in it before. This morning I went into that system's CMOS setup and turned off the "Wake on LAN" option, then shut it down and inserted the PCIe network card (the same JMicron unit I mentioned above). As soon as I switched on the main power switch (the one on the power supply), it came on, even though I have the option for restarting on power failure turned off. At the Intel logo screen, I pushed the regular power button, and it went off... and 2 seconds later started again. Again, I turned it off with the power button, and again it turned on in about 2 seconds. I repeated a third time just to be sure.
So I switched off the power supply (since that was the only way to get it to stay off) and swapped in the MassCool (sorry I had that wrong last time) multifunction card. This is a 2x RS232, 1x Parallel card from about a year ago which I've been stuck with, since none of the systems I tried it in would stay off. As I said before, all the systems I sell have Intel mainboards; the boards we were using then were DQ45CB, if that makes a difference. I had assumed this was a problem with the card until I tried a different brand and type of card and saw the same problem. With the MassCool card in place, the computer doesn't come on when you flip on the power supply, but once I push the power button to turn it on, pushing the button to turn it off doesn't work anymore; 2 seconds later it restarts.
At no time did I allow the computer to boot into Windows (never even saw the Microsoft logo screen) so I doubt strongly this is related to the operating system.
Thank you for that information.
Considering you've discarded an OS problem, the next troubleshooting step would be the power supply. This issue might be caused by a compatibility problem with the power supply itself, so testing a different one (different brand) would be a great troubleshooting step.
Also, you can test your system outside of the chassis. Please place your motherboard on a table, on a non-conductive material, and try booting it with only basic hardware attached. This is to ensure there are no grounding issues with the system case.
It's a case from Systemax, which we use exclusively; since we don't have problems with PCI cards, I don't see how that's going to be a grounding issue.
Having said that, I'll test it with a PCI card soon to ensure that's still true. But I'm not tearing systems which are basically ready to deliver apart to track this down... I'll just continue avoiding PCI-E cards. It's just a pain in the **** since there is only one PCI slot on the board.