When you tried to check disk of a partition of a hard drive on Windows, the system usually marks the partition dirty and the partition will be checked during the boot up process. Once the system finishes checking the partition, it marks the partition clean and the partition will not be checked again.
There are cases that after the boot time check disk is finished, the partition is still marked as dirty. This would cause the system to check the partition every time you boot the machine up. When I serviced a Dell Dimension E510 today, I took the hard drive out for backup. After putting the disk back to the computer, the system kept checking one of the partitions again and again. I then used the following command to clear the boot time check.
chkntfs /x D:
D: is the partition on my user’s machine, replace it with the actural drive letter for your system. On Vista or Windows 7, you need to invoke an elevated command prompt first to issue the command.