Everybody, THIS IS THE FIX for the problem:
How to make checkdisk (chkdsk) to run on boot:
**Please note, every time I say to reboot, that means you must SHUT DOWN your computer and wait about 10 seconds before booting it up again.
A restart will move the changes from session to session.**
The following steps must be performed to remove the dirty bit, and to enable chkdsk to access the drive:
1. Set your Diskeeper program to run a boot check -- Check every single value except for the a: drive, and set it for drive C:
2. Click the Start button on your taskbar, click RUN, and type in CMD. type in the command: "sfc /scanonce" without the quotes, and press enter
3. Go to My Computer, right click Drive C, and go to Properties. Click the Tools Tab and click Check Now. Select both checkboxes and set it. It will prompt you to run it at boot, say Yes.
4. Shut Down your computer, and then boot it back up again. -- **again, do not select RESET, but instead select Shut Down
5. Once the computer boots up, the chkdsk will Fail, then diskeeper will fail, then diskeeper will fail again. This is perfectly normal.
6. When the computer gets to the login page, please Log In. You will notice a scan for disk changes taking place. When it prompts you for the Windows boot disk, just say Cancel. After a couple Cancel's / No's, please click on the Cancel button of the scan. It will say something like are you sure, just say yes, and all the prompts will dissappear.
7. Open up Diskeeper once more and CLEAR all boot-scans on the problem volume.
8. Right click on your Drive C: and again click on Properties, click Tools tab and click clean now. Now this time only select the bottomcheckbox and scan the drive. This scan will start now, and will take about 15 minutes to run.
9. Once the scan has completed, go to your taskbar, click START, click RUN, and type CMD. Now please type in "fsutil dirty query c:" without the quotes and hit ENTER. It should say that Volume C: is dirty.
10. Now in the same window, please type "chkdsk /i" without the quotes, and hit ENTER. This scan will take about 10 minutes.
11. Once that scan has completed, please type "chkdsk /r" without the quotes, and hit ENTER.
12. Please shut down your computer.
13. Boot up your computer.
14. The chkdsk utility will run (5 layer scan, which takes about 1.5 hours), and the dirty bit will be removed.
15. You can now run disk defragmentor / diskeeper again.
16. If this guide did not work, please start again from step 1, as some instances require you to do the process twice.
I hope everything works out great for you, because I have tested this solution on multiple platforms and it has worked every time.