Start-up Repair failure, Problems Keep Piling Up

So I'll lay down the back story first. Months ago, randomly after a routine shutoff (no new programs installed, no power outages or crashes, just turned it off myself) Windows 7 would not boot, saying "Reboot and select proper boot device, or insert boot media in selected boot device and press any key." Happened for a day or two, I made a Windows 7 installation flash drive to boot to and do a Start-up repair, but on turning on the computer with the flash drive plugged in the issue vanished and Windows booted up successfully.

Fast forward to the present, where I decided to alter the Windows startup noise and login screen for an Avengers theme (using the instructions here Startup sound). On rebooting to see the effects, the "Reboot and select proper..." error occurred again. Made Windows 7 install flashdrive again, insert, problem persists. Followed these instructions to solve the issue (Startup Repair - Run 3 Separate Times) and on reboot the error changes to "Bootmgr is missing. Hit Ctrl+Alt+Del to restart." So I follow these instructions (Recovering the Windows Bootloader from the DVD - EasyBCD - NeoSmart Technologies Wiki) with no luck. Also, on and off throughout the repair process (and now permanently) the Repair center on the Windows 7 install flash drive has failed, saying ""This Version of System Recovery Options is not compatible with the version of Windows you are trying to repair. Try Using a Recovery disc that is compatible with this version of Windows." Therefore, I cannot complete a Start-up repair now. I am literally out of visible options at this point, and have never experienced such a complicated computer issue. If anyone can help me out, I'd really appreciate it!

Hello chubbedup and welcome to Seven Forums.

It sounds like you may have some damaged or corrupt system files. I'm not very hopeful that this will help, but you could try running a System File Checker scan from an elevated command prompt (option two.) If problems are noted, run the scan 3 times rebooting in between each scan.

SFC /SCANNOW Command - System File Checker

If SFC can't fix the problems you might consider a Repair Install if you can boot into Windows 7. You can't do a repair install at boot or in safe mode and I wasn't sure from your post if you can still boot into 7. But if you can boot into 7 and do a repair install it should preserve your user accounts, data, programs, system drivers, etc.

Repair Install

Thank you for the quick response! I apologize for the delay, busy weekend and did not expect such a fast reply. I cannot boot to Windows, so the Repair Install won't work. And due to the issue preventing me from using the System Recovery tools, the scan fails also, saying "the offline image has a different platform architecture than the running system. This is not supported for system repair." It's looking like a clean boot may be my only option.

Work through these steps for Troubleshooting Windows 7 Failure to Boot.

There is an installer ISO for your licensed version to burn to DVD or write to flash stick to try the repairs, and so you'll have it if you need to copy out your files and clean reinstall.

You'll need to do the disinfecting steps first since if it is infected it may not repair otherwise.

Thank you for all the replies guys, in the end I managed to backup files and clean boot. Problem solved!