Vista Startup Problems

I just went through a particularly bizarre sequence of creating a problem and fixing it, with Vista, that I thought I'd relate.

My freshly built Vista media center was giving me file system errors.  From the event log:

The file system structure on the disk is corrupt and unusable. Please run the chkdsk utility on the volume C.

Simple enough... "chkdsk /f c:".  It scheduled it for the next reboot, and I rebooted.

Instead of booting into chkdsk, the system booted to a black screen with a flashing cursor.  Hmm.  I left it that way for a while, but it wasn't doing anything.  A few reboots, then attempts to press F8 to get a command prompt, and nothing was working.

So I booted the Vista DVD.  It has a special repair menu now, and one of the options is to repair startup.  It promises to reboot your system several times, if required, to figure out why your system won't boot.  Sounded good - so I gave that a shot, and it worked!

Next reboot, it went through chkdsk and then booted.

But what I want to know is how did invoking chkdsk lead me to an unbootable system in the first place?