Booting Issues, new build

I just built my own PC for the first time. Everything went great all hardware compatible and software installed. After about a week or so my HDD keeps being disabled and I have to shutdown, disconnect it, reconnect and then sometimes it is found other times I have to do above mentioned process several times before drive is found or active. I thought it was the Intel rapid storage software, so I uninstalled that. Now randomly when starting up PC I get a message no OS found disconnect all drives that do not have an OS installed. OS is installed on SSD for quicker start-up. I disconnect my HDD, press control+alt+delete as it says on screen, computer restarts OS found PC works. Then I have to go through the process to get my HDD found or active. Some one Please Help.

OS: Windows 8.1 pro with media center
CPU: Intel Core I7-5820K Haswell-E
MOBO: Asus X99-Deluxe
PSU: Corsair HX1050W
SSD: Samsung 850 Pro Series 256GB SATA III 3-D Vertical Internal SSD
HDD: WD Red NAS 2TB Internal
Graphics Card: Gigabyte GTX 980 G1 Gaming
Memory: G.Skill Ripjaws 4 series 16 GB (4x4GB) DDR4 2800
Cooling: Corsair H105 Liquid cooler
Case: Corsair 760T
Optical Drives: Asus Black Blu-ray Burner (BW-12B1ST/BLK/G/AS) and Asus (DRW-24B1st/BLK/B/AS)
 
Any specific reason? I did forget to mention when the WD drive is not found, it does show up in the device manager as hidden. I don't think there is anything wrong with the drive if that is why you are saying to replace it.
 
If it is "hidden" in the device manager, there is a problem with the drive or the drive's connection SATA port. Try re-installing Windows or testing the drive if you can. Make sure it is installed as AHCI in the bios, and not IDE
 
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