BOOTMGR is Missing - Only Sometimes!

Update: trying the ideas above didn't solve the problem. I read what you mentioned about wiping the drive with the Diskpart command, but since I have KillDisk Pro, I thought I would try that. Since I didn't want to make a bootable DVD of KillDisk and be without my computer for hours (it took 29 hours), I took the drive, connected it to my SATA to USB adapter and ran the Windows version of KillDisk Pro and did a US DoD 5220.22-M erase of the drive.

The result? No BootMGR is Missing message, although during one of the reboots, it came up with "reboot and select boot device or insert boot media in selected boot device and press a key." I ran Windows 7 startup repair from the bootable DVD, and when it got to the part where it said "searching for Windows installations," it couldn't find any and said unknown OS. I ran a fix from the DVD. It said that if it was successful, the computer would restart and Windows would boot normally. Windows then booted normally, and when I ran the startup repair again just to double-check, it found my installation of Windows 7.

From what I've read, this "reboot and select boot device or insert boot media in selected boot device and press a key" message can occur if, during reboot, something as simple as a USB stick is connected to the computer. Is this true? Just to be on the safe side, I'm going to KillDisk the drive again (this time using a single pass of zeros), reinstall Windows and all my programs and settings, and make sure during all reboots that no other storage devices are connected to the computer.

Diskpart Clean Command can be run from the Win7 installer Command Line or System Repair Disk in less than 30 seconds and wipes anything that can interfere with the boot. This is why I suggested it since any longer method only serves to make data unrecoverable and has zero troubleshooting purpose. Sorry you chose another method which took 29 hours which is the grossest overkill I've ever heard of. I hate to think of how much your drive's life has been shortened.

If Startup Repair found your installation and repaired it after three recommended passes with reboots, then there is no point in reinstalling unless performance issues remain that call for it.

If you're ready to reinstall anyway then follow these same steps to get and keep a perfect Clean Reinstall - Factory OEM Windows 7

Thanks, Greg. I'll give Diskpart a try this time around. I'll keep you posted.

I couldn't figure out Diskpart, so I went ahead and used KillDisk again (one pass of zeros), which took ten hours. I reinstalled Windows 7, and had no error messages, but for the heck of it, inserted the Windows 7 boot disk, and immediately I could see the Windows 7 installation, and, of course, no problem could be detected. So, it appears the problem is solved. Thanks, guys, for all your help. This forum is a great service to PC users.