Windows 7 - No icon at login screen

Move the System flag back to 100mb System Reserved partition to run the Repairs again, if moving Active flag to C isn't going to start it after 3 Repairs rewrite the System boot files to C.

At this point everything possible that can be done is listed in Troubleshooting Windows 7 Failure to Start so I'd work down the list starting at the top now that you've tried the most indicated fixes.

For one thing it's possible you are infected so no repairs might work until disinfected.

If you get to the last steps to copy out your files and Reinstall to C follow the steps closely to get and keep a perfect install, then after its set up save a backup image so you never have to reinstall again.

I would not chance reinstalling to C without formatting to save your files in windows.old as it is too risky with that amount of files depending upon how important they are to you.

Now might be a good time to pick up an external for file and image backups.

Thanks for all the help. I ended up formatting my C drive and left my other drive alone. Almost everything in C ended up in windows.old and I just had to move everything back and reinstall updates. I got CCC again because it was needed for my GPU as it's my driver. What would you recommend me to do in order to prevent this in the future?

As stated before you do not need CCC bloatware which is problematic. You only need the driver, which should have come in on Windows Updates.

Did you first run all rounds of Important and Optional Windows Updates after enabling Automatically get recommended drivers and updates for your hardware (Step 3) as it says in Clean Reinstall - Factory OEM Windows 7 which is the last resort in the Troubleshooting steps? Only drivers still missing after all rounds of Updates should be imported.

If you ignored that and installed a bunch of drivers which Win7 may not want, then I'd do it over correctly according to the tutorial. Win7 is a driver-complete OS which decides what drivers it wants..