I know exactly what you are talking about! Sometimes after it does it on one of my machines, it tells me that Windows is not GENUINE!!! ***! So, I did some searching, and found out how to PERMINANTELY turn off the damn check disk FOREVER!
) (skip to step two...)
Here it is:
(1) In the system recovery options, I would like to suggest you launch Command Prompt and run the following command to check the hard disk.
Note: Please replace "C:" with the actual drive letter of the system drive on which Windows 7 is stored.
(2) If the hard disk is good, but it keeps checking the hard disk when starting, you may try the following commands to disable checking disk.
chkntfs /X C:
If you want to disable check disk on two or more drives, just keep on adding the drives:
chkntfs /X C: D: E:
This will disable check disk on C, D and E drives. Goodbye evil scan... Because if, like me, sometimes it won't even let me cancel by pressing any key! Plus I could not find a key on the keyboard labelled "any" anyway
Good Luck. This will fix it.