When I boot up or restart my computer, I sometimes get the countdown timer for running chkdsk and I usually bypass this and boot on into Windows. Is there a good frequency at which to allow your machine to run chkdsk or only when it's seriously needed to check the drive(s) for errors? Let me know if the specs of my machine are needed or if that is something that's not applicable to this question, thanks!
I'd ALWAYS do a chkdsk when a Windows system advises it be done....wait out the countdown and DO IT.
What this is telling you is that some file system structural error is likely on one of your disks (most likely C: if it is at reboot time) and that you CAN continue but you might further ruin your disk to the point where recovery efforts might not be possible.