Solved SOME Drives show in UEFI but not in Windows

Hi there,
I am hoping someone here can help:
I just picked up my new W8.1 computer from the store and started playing with it. I inserted 3 GPT Hard Drives. All three showed in the UEFI but only one of them showed up in Device Manager and in Disk Management. No matter what I tried, I could not get those other 2 disks to show up. Finally, I decided to re-load the whole darned thing from the recovery partition and re-load all drivers etc. Now all three Hard drives I had inserted showed in Windows. (I looked at all of them - all are fine - no Hardware issues)
However: I later changed the positions of the hard drives – i.e. the drive that WAS in slot 2 was moved to slot 1 etc. – I’m right back to where I was before: All three drives show in the UEFI – only one of them shows in Windows. This is my first machine with a UEFI. Is there something special that needs to be done to get those drives to show up in Windows?
One more thing: I also started the system using a bootable CD (Aronis recovery CD) and from here, all drives are visible.

you may want to look into your intel rapid storage technology settings

Check disk management, see if they show and all have drive letters assigned.

Update

@KYHI - I'm not sure I even have Intel rapid storage technology (or where I would even look for it)
I was unable to find anything that referred to it in Device Mangler.
The MSI motherboard ships with a utility called "MSI Live Update 6". This utility normally just crashes but if you do a "manual scan" on the MB driver only, it shows "Intel ME Drivers not installed" - It then downloads a file "Intel_ME_Drivers_10.0.028.1000" - It never installs that file. If I try to install that file manually, it tells me, a newer version is already installed.

@alphanumeric
To quote my original post: "...only one of them showed up in Device Manager and in Disk Management." - That's what this problem is all about.

@everyone
Some additional system info:
This is an MSI X99S Xpower AC (MS07881) board with 32Gb of DDR4 memory and a six-core i7 5930K CPU
Currently there is only one system drive (an SSD) connected. All the drives I am fighting with are "regular" hard drives that contain only data.

Further developments:
Switched the UEFI to enable "Windows 8/8.1 Features" (had no idea there was such a setting) also enabled "MSI Fast Boot" (which is supposedly faster than "regular" Fast Boot). Result: The system crashes as soon as more than one Hard Drive is connected.

from command prompt(admin)

type> diskpart
type> list disk

post pic

With the info you provided in the update > it appears you OS is setup in legacy mode..

another way to tell control panel > Admin tool > system info

View attachment 59869

@KYHI

Diskpart does not show the disks in question (see attachment)
It shows the SSD (119GB), one MBR disk (1.5TB), one GPT disk @ 2TB and one GPT disk @ 3 TB
2 additional 3TB disks are missing. (I had to disable the "Fast Boot" and "Win8/8.1 Features" options to be able to get back into Windows.

BIOS Mode shows UEFI (NOT Legacy or BIOS mode)

Support for the Intel® Rapid Storage Technology (Intel® RST)

View attachment 59881

Honestly not sure why drives not being seen by OS - but are being seen by firmware - so that tells me the SATA ports are active

The documentation for RST at Intel® Rapid Storage Technology (Intel® RST) — Supported Chipsets and Controller Hubs does not list the x99 chipset my board uses.

Since everyone appears to be fresh out of ideas, I am marking this thread as solved