It is not malware, but my honest best guess would be a fundamental issue with a registry hive.
If the hive is imperfectly formed, it is re-read imperfectly. So a perfectly fine registry correction is imperfectly saved at exit.
I would do a registry repair at this point. I gave you (two messages above) a rather plain English method described by Pete White. The MS KB equivalent:
It is perfectly possible that a good registry cleaner utility will advertantly or inadvertantly correct a minor registry issue such as this.
Because fundamentally, the issue is either a true hard error on the hard disk, and the dirty bit is being set repeatedly by the OS for good reason; or it is an indication of a bad registry hive.
If it was my computer I would:
. download the free diagnostic/setup disk utility from the exact hardware manufacturer of my hard disk drive. I would run their non-destructive testing and see what happens. If errors were thrown, I would call them for replacement of the hard disk under the in-place swap program, where I gave them a credit card, they sent a new drive, and I copied everything from old --> new drive (likely using the same downloaded utility);
. if the drive failed the manufacturer diagnostics, I would replace the drive immediately, using the same plan;
. if the drive repaired without serious issue, I would do nothing more;
. if the autochk issue repeated on any reboot soon after, I would repair the registry hives.
I sincerely hope this helps your circumstance,
Bill Castner