Windows 8.1 stopped booting when other hdd's are connected

[keyboardsmash]

Hello,
I've got Windows 8.1 Pro x64 installed for a month now and up until today everything was running smoothly.
Today the Os will not boot though, the boot process hangs during the loading animation, similar thing happens, when I try make a new install or repair the system using the repair tools from the dvd - when I click "Repair Tools" or "Install" nothing shows except for the blue background.
The problem goes away, when all other drives, except for the one with the OS, are disconnected.
I use a following build:
MB: Asus Maximus VII Gene
Drives:
- Plextor m6e m.2 pci-e ssd<- Windows 8.1 installed
- 4 x WD Green as archive
- Crucial m4 SSD for vm's
Removing all drives except for the helps, however that is not really a solution. Disabling the SATA Ports does not help either, they have to be physically unplugged.
Also! - after disabling the Plextor drive an keeping the other drives connected, right after POST there is a message about a missing windows bootmgr. It's in my native language (now I have 8.1 en_us, a month back I had another installation on the Crucial ssd), so it seems the second bootloader is somehow interfering (?) although like I said, everything was running with no problems for a month.
I should also add, last time, before the 8.1 installation on the plextor ssd, I have wiped the crucial ssd using the erase ssd bios function, so all previous boot information should be gone.

How can I fix booting 8.1 again with all drives attached?
Thank you!

Scrrenshots:
http://imgur.com/a/rBQK6

SOLVED:
Had to do a format :drive /p:2, that is format with zeroing out the secondary flash drive which still had some boot loader, that activated randomly screwing up the system boot. Turns out the Asus Flash Erase is worth sh*t.

 

[keyboardsmash]

see edit

 

[johnbl]

most likely had a primary partition that was marked active on it.
when you plug it into another system with another primary active partition the system will try to assign drive letters and often it ends up changing the drive assignement for your boot drive.

I would think a erase program might erase the files and write over them but unless it deleted your actual partition you would still have this problem when you plugged in the device.

or it could be a bad program, don't know i have not used it.

Hello,
I've got Windows 8.1 Pro x64 installed for a month now and up until today everything was running smoothly.
Today the Os will not boot though, the boot process hangs during the loading animation, similar thing happens, when I try make a new install or repair the system using the repair tools from the dvd - when I click "Repair Tools" or "Install" nothing shows except for the blue background.
The problem goes away, when all other drives, except for the one with the OS, are disconnected.
I use a following build:
MB: Asus Maximus VII Gene
Drives:
- Plextor m6e m.2 pci-e ssd<- Windows 8.1 installed
- 4 x WD Green as archive
- Crucial m4 SSD for vm's
Removing all drives except for the helps, however that is not really a solution. Disabling the SATA Ports does not help either, they have to be physically unplugged.
Also! - after disabling the Plextor drive an keeping the other drives connected, right after POST there is a message about a missing windows bootmgr. It's in my native language (now I have 8.1 en_us, a month back I had another installation on the Crucial ssd), so it seems the second bootloader is somehow interfering (?) although like I said, everything was running with no problems for a month.
I should also add, last time, before the 8.1 installation on the plextor ssd, I have wiped the crucial ssd using the erase ssd bios function, so all previous boot information should be gone.

How can I fix booting 8.1 again with all drives attached?
Thank you!

Scrrenshots:
http://imgur.com/a/rBQK6

SOLVED:
Had to do a format :drive /p:2, that is format with zeroing out the secondary flash drive which still had some boot loader, that activated randomly screwing up the system boot. Turns out the Asus Flash Erase is worth sh*t.