MSI Z87I Won't Reboot or Shut DOwn

Question

My new system won't shut down or reboot from the OS (Ubuntu 14.04) or from the BIOS settings, i.e. Settings -> Save & Exit -> Save Changes and Reboot will not reboot the system. All my peripherals will turn off, but the fans stay on and the only way to power off the system is to long-hold the power switch on the front of the case or turn off the power at the PSU.
There is ONE case in which the system will reboot. If I go to Settings -> Save & Exit, choose "Restore Defaults" and then select "Save Changes and Reboot," the system will reboot one time, but it won't reboot or shut down after this.
I'm already on my second MoBo since I thought it was a MoBo issue.
Specs:
SSD: Patriot Pyro 60GB
Memory: 2x PNY 4GBH2X02E99927-16-H
CPU: Intel Core i3-4150 LGA1150
PSU: Thermaltake TR2 500W
I've tried reseating the MoBo as well as testing it outside of the case with no luck.

Answer 1

Quote from: rusty.carruth on 10-January-15, 07:52:22
Ah, thanks!  Got it.
It looks to me like that is a different link to the same program, as when I downloaded it I got 'MSIHQ Tool 1.25g Installer(1).rar' as the filename, since I had just downloaded 'MSIHQ Tool 1.25g Installer.rar' from the link I posted (or perhaps from a page pointed to by that page, I've already forgotten where I got it...)
I notice that the '180' file has a batch file that runs 'fpt'.  Am I supposed to run that batch file, or run 'efiflash bios.bin'?  (Or both if this is the first time I've flashed the motherboard)
Quote
It looks to me like that is a different link to the same program, as when I downloaded it I got 'MSIHQ Tool 1.25g Installer(1).rar' as the filename, since I had just downloaded 'MSIHQ Tool 1.25g Installer.rar' from the link I posted (or perhaps from a page pointed to by that page, I've already forgotten where I got it...)
em nope, its the same program. (1) is auto renamed because the same name was already existing in your download folder
Quote from: rusty.carruth on 10-January-15, 07:52:22
I notice that the '180' file has a batch file that runs 'fpt'.  Am I supposed to run that batch file, or run 'efiflash bios.bin'?  (Or both if this is the first time I've flashed the motherboard)
no need to run anything
just let the tool to prepare the USB key then boot from it
when this menu appear select option 2:
1 Run Memtest
2 Proceed with BIOS Update
3 Flash back to prevision bios
then press any key after read some safety instructions
then when asked if you want to Run Memtestx86, answer with "N"
then flash will start and will be asked for reboot when its done
you no need to type or run anything manually, its tottaly automated