I had the same problem with my Win7 install. Root cause was a problem with a corrupted AVG 8.5 log file. On reboot, system would hang at 1 second countdown to run chkdsk. Here's the fix for clearing the dirty bit and running chkdsk.
1st - go to control panel - backup and restore - create system repair disk (if you haven't made a disk image...now would be a good time.
2nd - boot to system repair disk. choose command prompt option
3rd - at dos prompt type chkdsk c: /f
let it run... mine looked like it was hung up during stage 3, but eventually it will complete
4th - reboot. my chkdsk countdown timer appeared and completed by itself. system now reboots without the
chkdsk prompt/timer on several tries.
Hope it helps.