W7E x64 will not boot after adding a hard drive

I have a Windows 7 Enterprise x64 system up and running with no issues. This computer has a 240Gb SSD and a 3TB HDD. The entire Windows system is on the SSD together with a data partition, the 3TB disk is merely for storage. The system boots and works ok either with the SSD alone or with the SSD+HDD. Both these disks have GPT partition tables and the system boots in UEFI mode. Up until here all is well...

I have another 2TB HDD I use for backups. I have SATA and power cables dangling just outside the case and I occasionally connect this disk to take backups of important stuff (hot-plug, this works fine). I later disconnect the disk and store it elsewhere.

The issue that is bugging me, and I understand it is not extremely serious, but still I believe it shouldn't happen, is that if I try to reboot the system while the last disk is connected Windows will refuse to boot. It'll fail into a white on black text screen saying it cannot find the system device or whatever. With all the updates and the fact that most of the time I use the system remotely it can be quite a pain.

I have a USB drive with the recovery tools. When all the disks are connected it boots but refuses to work, says my version of Windows is not supported (tried both UEFI and legacy boots of the USB). When the last disk is out, it runs just fine but obviously Startup Recovery says there are no issues which under that configuration is true, the system also boots fine.

I read about the physical SATA port numbering being a possible reason, made sure the SDD disk is on the first port, same behavior.

Checked the BCD entry, it calls for the first physical disk. The SSD shows as id 0 either with or without the backup HDD

I removed any traces of boot loaders, boot managers, active flags in partitions, anything like that on all disks but the SSD. The backup HDD is old-style MBR partiion table. I am willing to convert it to GPT if it can be done keeping the data and someone has a good reason to think that may be it.

I even went ahead and installed linux hoping GRUB2 would take over some important part there but after selecting Windows the same thing happens (everything works fine without the backup HDD now with dual booting etc). I kinda knew this wouldn't help but had a spare partition I was reserving for Linux so I gave it a try.

So, it's beyond me, why Windows would care about a new disk being present to boot. I thought that UEFI+GPT would've been the end of all this nonsense, the partitions having those big unique ids and all...

If anyone has any suggestions I am willing to try them!

Thanks

Code:

Windows Boot Manager
--------------------
identifier              {bootmgr}
device                  partition=\Device\HarddiskVolume1
path                    \EFI\Microsoft\Boot\bootmgfw.efi
description             Windows Boot Manager
locale                  en-US
inherit                 {globalsettings}
default                 {current}
resumeobject            {a82a70cc-8ff4-11e3-8cfd-8275518eaedd}
displayorder            {current}
toolsdisplayorder       {memdiag}
timeout                 30

Windows Boot Loader
-------------------
identifier              {current}
device                  partition=C:
path                    \Windows\system32\winload.efi
description             Windows 7 Enterprise
locale                  en-US
recoverysequence        {a82a70ce-8ff4-11e3-8cfd-8275518eaedd}
recoveryenabled         Yes
osdevice                partition=C:
systemroot              \Windows
resumeobject            {caea0dc5-d516-11e5-bfc3-806e6f6e6963}

Code:

Disk /dev/sda: 223.6 GiB, 240057409536 bytes, 468862128 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: 9B921798-4B5C-4228-AC98-B2062F2C3BFC

Device         Start       End   Sectors   Size Type
/dev/sda1       2048    206847    204800   100M EFI System
/dev/sda2     206848    468991    262144   128M Microsoft reserved
/dev/sda3     468992 168241151 167772160    80G Microsoft basic data
/dev/sda4  168241152 189212671  20971520    10G Linux filesystem
/dev/sda5  189212672 468862094 279649423 133.4G Microsoft basic data 

Disk /dev/sdb: 2.7 TiB, 3000592982016 bytes, 5860533168 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disklabel type: gpt
Disk identifier: 4B7579B3-CCC9-4A00-9EC7-C46A672220D4

Device         Start        End    Sectors  Size Type
/dev/sdb1       2048     206847     204800  100M EFI System
/dev/sdb2     206848     468991     262144  128M Microsoft reserved
/dev/sdb3     468992  105326591  104857600   50G Microsoft basic data
/dev/sdb4  126093312  230950911  104857600   50G Microsoft basic data
/dev/sdb5  230950912 5860530175 5629579264  2.6T Microsoft basic data 

Disk /dev/sdc: 1.8 TiB, 2000398934016 bytes, 3907029168 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x0b7a9d21

Device     Boot     Start        End    Sectors  Size Id Type
/dev/sdc1            2048  111472319  111470272 53.2G  7 HPFS/NTFS/exFAT
/dev/sdc2       111472320  115666623    4194304    2G 93 Amoeba
/dev/sdc3       115666624  230725529  115058906 54.9G  7 HPFS/NTFS/exFAT
/dev/sdc4       230725530 3907024064 3676298535  1.7T  5 Extended
/dev/sdc5       230725593 3907024064 3676298472  1.7T  7 HPFS/NTFS/exFAT

Hi, the boot order in the firmware is set to boot "Windows Boot Manager" (this is UEFI, not BIOS). There is no USB disk in this scenario (apart from the recovery tools which I removed after attempting), the new disk is "external" only in the physical sense meaning it is actually outside the case but it is a standard 3.5' disk connected to a normal internal SATA port.
I can request the boot menu when the computer powers on and manually select the same option and the same issue still happens.
I believe that part of the boot is fine, UEFI finds the Windows Boot Manager in the EFI partition, loads it and passes control to it, the error message I get is from this boot manager saying it cannot find the "Windows System" volume.
Just to be sure I have removed any active partition flags in the new disk as well as any bootloaders, the disk just has plain data.

Thanks

Ok, I cracked it... well, surely not the "why" but at least I got it to work good enough for me.

This is what I did:

With the idea that maybe it was the MBR vs GPT partitions I decided to do some tests. I wasn't about to lose my 2Tb of data in this disk nor did I have an easy was to copy it elsewhere, so I dug around and found an old 160Gb HDD which I recluted to be my guinea pig.
My first objective was to replicate the problem with this disk. I wiped it clean, created a single NTFS partition and formatted it, rebooted with the disk connected and to my surprise Windows booted without issues. So, it's not the "MBR partition table" at fault. I decided to replicate a very similar partition table as in the real disk, created three primary partitions, the extended and one logical drive, rebooted... bam! failure.
So, good, I have the same issue on a disk I can play with. With a single partition it boots, with five it doesn't, I just started working my way down then.

First thing to eliminate was the extended partition, move from 5 to 4. I did this, removed the logical one, the extended one and created a last primary partition... booted fine!

It seems Windows is, for whatever strange reason, not playing well when there is an MBR disk with an extended partition on a system that has UEFI boot on a disk with GPT... could it be because all GPT partitions are "primary" and the presence of an extended partition messes something up? no idea... but here I stop caring

I went back to my real disk and decided to re-create the logical volume as a primary partition (this much I am confident of doing without losing data, just match the start and end sectors). I did this, rebooted and Windows loaded perfectly without a hitch. I can now use my computer normally when this backup disk is attached (not that much to ask for, right?)

Anyway, I wirte all of this in case someone else comes across a similar issue. I know I searched and searched before posting and nothing so hopefully this may help someone.

New partitions on my backup disk (in contrast to what was in the original post):

Code:

Disk /dev/sdc: 1.8 TiB, 2000398934016 bytes, 3907029168 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x0b7a9d21

Device     Boot     Start        End    Sectors  Size Id Type
/dev/sdc1            2048  111472319  111470272 53.2G  7 HPFS/NTFS/exFAT
/dev/sdc2       111472320  115666623    4194304    2G 93 Amoeba
/dev/sdc3       115666624  230725529  115058906 54.9G  7 HPFS/NTFS/exFAT
/dev/sdc4       230725593 3907024064 3676298472  1.7T  7 HPFS/NTFS/exFAT