To disable automatic disk checking at Windows startup through registry, go to the following registry key:
In the right hand pane, double click BootExecute.
The default value of the key is autocheck autochk *
* means every drive is checked for consistency. Just add /K:C at the end before *. /K switch will disable autocheck on C: drive at Windows startup. So the final value should look like this:
autocheck autochk /k:C *