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Do you have the Default Power Settings to Sleep rather than shut down?
What happens when you press the Power Button on the Case?
What Case?
Are the Case Headers on the right way that is Pin 1 to Pin1?
Remove them and see if you can turn on and off the Computer from the MB.
 
 
Asus Zenith Extreme x299 or Asus Zenith Extreme x399 AMD MB?
I am Not Finding the "Asus Zenith Extreme x299" Motherboard.

This must be your MB Asus Zenith Extreme x399 AMD Correct?
Are Both 8-pin EATX 8 V Power connector Connected?
Take the MB out of the Case and Bench Test it.

You may want to Edit your Topic Title. You can Edit your First Post to do this.
X299 is an Intel Chipset Motherboard.
 

pisymbol
Yes and yes. I can't bench test it now.
 
I've been told that it could be an issue with the PSU (though I doubt it myself but I'm the only one with this issue and the only variable different is the SuperNOVA).

 
Who told you this?
Turn Off the ECO Mode....
 
I have seen this issue with Bent CPU Socket Pins so you may want to remove the CPU and check the Socket Pins.

Yes I did see the Video on install that CPU, it is a Bear.

What's funny is ErP mode is ON and turning it off helped a little (now the LEDs on the board go out).
 
The problem is I don't have a spare PSU with enough juice. Maybe EVGA will RMA this PSU on good faith?
 
Asus seems to believe it is my PSU causing the problem.

Sounds like a faulty psu to me.

Looks like it is indeed the PSU. A buddy lent me a 650G2 and the box powers off without issue. You can tell instantly as when I power on the system, the CPU fans and such stay off until I hit the power button. The box POSTS normally and then I hold the power button down and it turns off normally. With the 1200P2, the box stays on and the CPU fans run ad infinitum (I waited 5 minutes which is long enough).
 
Note: For the 1200P2 I tried ECO mode on and off and it still has the issue. I guess it's RMA time. Kinda surprised this happened. Bought from Newegg.

I'm a bit worried that there is some incompatibility with the supply and the BIOS though...but perhaps not...

Question, could this be a bad motherboard PSU cable? I read a thread that had a similar problem and the fella's solution was to replace the motherboard power cable. Anybody seen that before?

The 650 and the 1200 are NOT the same cable. The 650G2+ is one piece while the 1200 is two for the MB. It won't fix.
 
In progress...

bcavnaugh
P/N: 100-CK-1300-B9 G2/G3/P2/T2 Black Power Supply Cable Set (Individually Sleeved)The above kit is for both PSU the 650 G2 and the 1200 P2 The Motherboard 24-Pin Cable is the same.   

Alrighty. Let me see if I can borrow the cable again. The one I HAD that my colleague gave me with the 650G2 did not fit the 1200P2.

In Red, the CPU Power Cables are also the same as the rest between the two Power Supplies.

 

Nope.
 
The power supply is this one:
 
https://www.amazon.com/EVGA-SuperNOVA-NEX650G-Certified-120-PG-0650-GR/dp/B009YC3DKY
 
Notice the back is different. Sorry for the confusion. I disconnected the A in that diagram as well as the SATA connector it uses for power and that does not help.
 
With the 650 supply, I can power up and power down the system normally (at least with the power button, I never booted an OS because that in itself is different that what the 1200P2 does). I did have to take disconnect the Titan Xp in it because it doesn't have enough juice.

Yes. Again, sorry for the confusion.

Well, that's major suckage.

Something that jumps out at me is the SuperNOVA 1200 P2 is ErP compliant and the SuperNOVA 650 PG is not..Thinking that a piece of hardware may be the issue and keeping the board alive.

I'd clear CMOS and enable ErP Mode and disconnect everything (all fans/fan cards including CPU, lights, front panel/Q-Connector, USB devices including keyboard and mouse, accessories, everything except CPU and RAM and graphics card and boot drive), put all switches and jumpers back to default configuration and see how it rolls..Use the mobo button to turn it on/off..If it works OK, then start connecting things one at a time until the problem returns..Your board should probably boot into Windows without a graphics card installed too like my board does (listen for the Windows start up sound after enabling it in Sounds and unchecking 'Turn on fast startup'), leave speakers/headphones connected, might try that also.

You'll need to set the CPU fan to 'Ignore' in the BIOS Monitor menu or it prolly won't boot if it detects a CPU fan is not present, it'll cough up an error.

Uncheck 'Turn on fast startup' in Windows -> Control Panel -> Power Options -> Choose what the power button does -> Change settings that are currently unavailable..Might give this a go first..You can also show/hide Sleep and Hibernate in the Power menu.

Read through your thread over at ROG but can't remember all the stuff you tried already..LOL.
 
Good luck.