Autocheck always runs at boot.  Only if it detects that the dirty bit has been set on a partition (indicating an abnormal shutdown of the system OR that the file system has detected an inconsistency during normal operation and automatically scheduled chkdsk to run) will it actually run CHKDSK on the indicated partitions. Chkdsk as run by Autocheck does not do as comprehensive a repair as chkdsk /r.

PerfectDisk is first in the bootexecute list.  When the system boots, here's what happens:

- PD's boot time defrag code runs.
- It looks to see if it is even supposed to run.  If not, it exits.
- It checks to see if the dirty bit has been set - if so, it exits to let CHKDSK run.
- If volume is "clean", then PD performs it's own consistency check of the file system to make sure that things are "ok" (as CHKDSK doesn't always fix errors with the file system).  If this check passes, then PD's boot time defrag actually runs.  If not, then it exits.