To prevent running scandisk after a bad shutdown do this:->
Click "Start", then "Run", then type "msconfig" ...then at the bottom right click "advanced"...put a check beside "disable scandisk after bad shutdown"...reboot. Then if it is important to you that scandisk runs after a bad shutdown (I find it annoying) try unchecking the box again and see if that fixes the problem.
For chkdsk, Not 100% sure but i believe chkdsk puts a flag in your pagefile to run at startup...go to admin tools/local security/security options and enable the shutdown option to clear virtual memory...then reboot and see if that fixes you up or not...
Otherwise, "chkntfs /x" will stop the chkdsk from automatically running...
If that doesnt help, then have a look here:->
HK_Local_Machine>Software>Microsoft>Windows>CurrentVersion>Run
HK_Local_Machine>Software>Microsoft>Windows>CurrentVersion>RunOnce
HK_Local_Machine>Software>Microsoft>Windows>CurrentVersion>RunOnceEx
and less likely:
HK_Current_User>Software>Microsoft>Windows>CurrentVersion>Run
If that doesnt help, follow these steps:-
1) Using the RecoveryConsole, Rename c:\windows\system32\autochk.exe to autochk.old.
2) Restart your machine.
3) If you are handy with the registry, >>Start>>Run>>Type "regedit">>Enter
4) Back up registry first.
5) Then search for "autochk" in the registry and find where it autoloads.
6) Remove it from this registry key and all others that may reference it.
7) Reboot and see if this has gotten rid of your problem!