Solved CHKDSK never fixes & chews up drive space.

I'm having a really hard time with my computer. I'm trying to repair windows before I make an image and transfer it to a new drive. This drives circuit board failed which caused windows to keep dropping it and running disk repairs.

Now that the board is replaced, after fixing the missing boot info, it seems CHKDSK wants to constantly run on boot. I don't think it's every single time though I could be mistaken. I'm avoiding rebooting. When it does run, it finds the same problems each and every time. It keeps deleting the same index entries and recovering the same orphaned files. All of the recovered orphans have a corresponding deleted index entry.

I found a thread on the WindowsSeven forum that suggested a problem in System Volume Information in that CHKDSK is case sensitive and could be causing a problem. (Check Disk (chkdsk) - Read Event Viewer Log - Windows 7 Forums). In an attempt to follow those instructions I found that my System Volume Information folder has grown to 64.5 Gb. It seems every run of CHKDSK causes a new System File to be created that's anywhere from 1 to 17 Gb in size. I'm losing space on my hard drive with every reboot.

Can I delete these errant System files?
How can I fix CHKDSK so that it stops trying to fix the same files and entries over and over again?

ADDENDUM: It just got worse. I had followed the instructions to take ownership of the System Volume Information folder. While I waiting for a response here, I gave ownership back to the Administrator account, but the permissions are all still set for me. I didn't have these permissions before. I shouldn't have access to this directory, right?

I've figured out the large system files and am left with a simpler problem. I've marked this one solved so I can restate the problem in a new thread.