It really depends on which action has been selected for the boot time scan: If it is to simply repair the drive (/f), then you may have an issue. However, if the option to fix and attempt recovery of bad sectors is selected (/r), then that would explain the long wait time. For that process to finish on my laptop, it takes well over 5 hours! It also seems to hang indefinitely at 10% then jumps right to 100%. My suggestion would be to wait, depending on, if you did choose, the option you chose for the boot time scan.