So I just upgraded to Windows 8 and here is an unusual problem I ran into.
I installed Windows 8 on a new hard drive. I had no problems installing and used the new OS for 24 hours without issue. The next day I installed my old drive as drive G: and I wanted to delete the old Windows installation. No matter what I tried I could not change the permissions to allow me to delete the old Windows install. I found a tip to boot to a command prompt using a Windows CD and I should be able to delete it from there. I used a Windows XP disk and booted to the repair console (pressing R at the first menu) from there I was able to navigate to the G: drive, confirm I was on the old hard drive and tried the command rd /s /q "G:Windows" to remove the old directory. It did not work and I was given "Access Denied" message. Maybe I had done something in my many attempts to gain permissions over the folder inside Windows... anyway, I gave up and reset the PC to boot back into Windows 8. That's when the trouble started.....
I quickly received a blue screen telling me there was a problem booting and I needed to run repair using the original Windows DVD. I received the error 0xc000000e and I was informed that an important file was missing: windows/system32/winload.exe
Any attempt to repair the problem using the Windows DVD failed instantly with just a message that the system could not be repaired. I even tried the refresh and reset options (to delete all files and updates) but all failed instantly. The only option that worked was the command prompt where I noticed something interesting.... the C: drive was empty! My Windows installation and files were all on the D: drive. That isn't good. It's very important that the Windows installation is in the C: drive!
I booted the PC using Acronis Disk Director software to see that my drive had 2 partitions. Both partitions were set as active and primary and the C: partition was only about 350MB. I deleted the partition and rebooted the PC. Again it complained that there was a problem but it was able to Auto Repair without the need of the original DVD. After a couple of re-boots the PC booted correctly. All of my files and settings were just as they were before the problem.
My victory was short lived because I then installed a new raid hybrid card to run a SSD and HD as a hybrid drive. On my next reboot I ran into the same issue! error 0xc000000e and again the partition I deleted was back and set as primary. This time I tried more drastic measures to delete the partition and ended up damaging my windows installation too. Luckily I had made a disk image of the installation and I was able to restore from my backup.
I read that the mysterious partition called "System Reserved" is something that windows 7 creates when installing a fresh copy on a new drive. Apparently Windows 8 does this as well. It is not required to use windows but I read that it is used for BitLocker. I'm still not sure exactly what is causing this partition to become active primary. At first I thought it was the old Windows XP CD that I used to get to the command prompt but I did not use this CD the second time. I believe now that the problem may be related to the old drive being put back in as a secondary drive and when a Windows repair action is performed it sets the System Reserved partition as active.
If anyone encounters the same or similar issue... please post a comment letting me know what you found.