Windows tries to perform chkdsk on every boot but fails

Hello everyone.
Today my computer froze upon exiting Battlefield 3 and had to shut it down manually.
After a lot of problem solving (I had to change the hdd port on the m/b) I am left with the problem displayed in the attached image and cannot figure out what to do. I have searched around and tried a lot of repairs but nothing happens. I also run sfc / scannow command several times (in safe mode also) which finds some problems that cannot be fixed.
Any help would be appreciated.
The ultimate solution would be to format my ssd and hdd

Report back what happens when you attempt to F8 boot into Safe Mode.

It boots in safe mode. Nothing out of the ordinary happens.
I have to mention that the computer boots normally to windows after the attached message goes away.

What disk is it trying to check? Open an elevated command prompt and type in fsutil dirty query c: (change the driver letter as required for each driver you have).

Boozad said:

What disk is it trying to check? Open an elevated command prompt and type in fsutil dirty query c: (change the driver letter as required for each driver you have).

Just run the command you suggest on my two drives and reports that both are NOT dirty

Run chkdsk on the non-system drive via command prompt. Disk Check

Boozad said:

Run chkdsk on the non-system drive via command prompt. Disk Check

just did. It force dismounted the drive, performed the check and found no problems.
I just did sth else. I found in task scheduler the entry about autochk and deleted it. I will reboot now and report back.
I found an article in ms kb about it but I don't know if I will fix the problem or simply hide it.

Edit:
Just tried this https://support.microsoft.com/en-us/kb/831426 but still no luck. It tries to perform the check at evey boot

I found the following Microsoft link, you may not like the answer found in here:
"http://microsoft.com/en-us/windows/forum/windows_7-windows_programs/"
"how-to-disable-the-chkdsk-check-disk-on-start-up/35f58c69-7a6c-4e1b-aec3-26d7131ec643"
For some reason, link does not display properly, copy and paste both pieces into your browser address field, then remove my quotation marks, and remove the space between programs/ and how-to-disable
--- that link works in my FF, but won't correctly post in here.

I will try this, this afternoon.
My main concern is the volume drive it tries to check. What drive is this? Could it be the system reserve disk?
I recently installed an ssd but for some reason the system reserve partition was installed on my secondary mechanical drive. I think it had to do with "F6" drivers....