The only thing I can suggest is this...
Under the following key in the Registry, make sure the "BootExecute" Value Name has a Value Data of...autocheck autochk*
HKEY_LOCAL_MACHINE | SYSTEM | CurrentControlSet | Control | Session Manager
...The binary "Value Name" in the RH pane will be "BootExecute" (without the quotes). Right-click the "BootExecute" binary name and select "Modify" (if the value is something other than...autocheck autochk*) and type in the correct value as I've shown it below.
Under the "Value" tab, it should look like this...
autocheck autochk*
Reboot for the change to take effect, and see if chkdsk still runs automatically...after modifying the above value.
