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Hard Drives Not Detected In BIOS but SSD Is


I recently replaced my old 600w power supply with my new 650w SLI ready one to get my GTX 970s working in SLI and now encountering a world of problems but the main one for right now is the HDDs...
I booted into windows after getting everything set up and working but after running a program called DifferentSLIAuto and the install.cmd it put my computer in test mode and after a reboot my HDD's were not able to be detected in my Bios or operating system. The only 2 drives that are still detected are my flash drive and SSD. 

I don't believe it's a power issue because I tried with both power supplies and 2 sets of cables and it still didn't work. I also don't believe it's a motherboard issue because it was just fine until I rebooted and I didn't touch the hardware. 
I think it's a software issue or something but idk what the hell that program did to cause this.


My Specs

CPU - AMD FX 8350 Stock

CPU Cooler - Hyper 212 EVO

GPU - EVGA GTX 970 SSC x Zotac GTX 970

Mobo - Gigabyte GA-990FXA UD3 Rev.4.0

PSU - [Current: EVGA NEXG650G 80+ Gold 650w] [Old: Corsair CX600m 80+ Bronze 600w}

RAM - G.Skill Ripjaws X Series 8GB 2x4 DDR3

SSD - Samsung 850EVO 250GB

HDD1 - Seagate Barracuda 2TB 7200RPM

HDD2 - HGST Hitachi 2TB 7200RPM

HDD3 - Seagate 500GB 

HDD4 - Random one I took out of a laptop

OS: Windows 10 Pro 64bit

BIOS: Latest F3 version 



This may be irrelevant but when trying to use DifferentSLIAuto I got that [E] : Could not find patch #3. Please inform Ember @ techPowerUp! forums. error and tried a workaround where I ran install.cmd in an elevated command prompt and then I rebooted. After doing that is when the problem started. 

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