Frustrated with new setup - pc won't shut down and more (GA-X99)

[ohpro]

Hello,
I built 3 weeks ago a new system based on Gigabyte board and Iv'e got many problems.
CPU: i7-5960x MB: GA-X99-SLI (switched to GA-X99P-SLI), Toshiba M.2 RD400, Quadro k4000, 64gb DDR 4, 1050W PSU, LSI MegaRaid 9271-8i.

I already replaced the motherborad once from GA-X99 to GA-X99P (still have problems), I replaced the Toshiba RD400 to a new one (still have problems), I replaced the PSU to a new one (still have problems)

1. PC was shut down randomly on windows 10 (64 bit), Event ID 41 on event viewer - I replaced the PSU and it seems to solved the problem (running for 3 days with)

2. PC won't shut down, the case cables checked, I've tried this with 3 different PSU, I disabled the ErP, updated the bios to F23 - It doesn't matter if I click the power button on the case or via windows shut down option - the screen is off but fans and leds still on, this is also happen when trying to turn off during boot so I know this is not windows problem. the only why to totally shut down is switch off the PSU power button or unplugging the cable.

3. I have LSI 9271 raid controller - worked perfect on previous machine. When I insert to PCI the system freeze during boot.

I almost replaced every component in this machine, i've updated the bios, reset CMOS, installed more than 10 clean WIN installations. Nothing helps. Please, I need your help :/

Thanks

[dmdilks]

Have you try to run it outside the case to see if it something to with the case?

[ohpro]

Nope,
I tried to reconnected everything inside the case so I guess that's not the problem.. It is also a new case