It was not able to get full access at startup. Zone Alarm is known to cause this. Defragmentation utilities that have a boot-time defragmentation option will do this. Several Antivirus programs will do this.
You could use MSCONFIG, click "Use Diagnostic Startup", then reschedule the chkdsk operation and reboot. Depending on how aggresive the firewall, defragger or AV program is, this may let you get the chkdsk to run. Remember to reset with MSCONFIG for a normal startup.
Or, use Recovery Console and do a chkdsk /r from that session. No reboot required.