I have a dell laptop with similar behaviours.  However, I can fix it by
modifying the PCI register offset 0xA4  on LPC (ex. 00:1f.0 ISA bridge).

You can use lfdk (see http://alexhungdmz.blogspot.tw/2015/06/uitlity-
reading-and-writing-pci-io-and.html) to modify the PCI register.  Please
change BIT15 of 0xA4 (more BIT7 of 0xA5).  For example, it was 0x28 and
I modified it to 0xB8 (please refer to attached screenshot).

This bit (called PME_B0_S5_DIS) is reset by RTCRST# (RTC reset) and
normally that does not happen.  It will stay as long as RTC has power or
is written by again.

I can also check your PCI registers if you can upload output of "sudo
lspci -xxx"


** Attachment added: "pci.png"
   
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1457852/+attachment/4446781/+files/pci.png

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Title:
  [Dell Optiplex 9020] Shut down causes restart if USB3 enabled

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