Sorry Richard, I don't think I have explained myself very well.
Let me try again. This all started with a right click in explorer on the c drive, select properties, then select tools, then select Error checking, check now
Ticking the Automatically fix file system errors results in the message "The disck check could not be performed becuase exclusive access to the drive could not be obtained. Do you want to schedule this disk check to occur the next time you restart the computer?" and then clicking on yes.
I understand this is all normal windows behaviour up to this point, but where it goes wrong is on the next reload. You would normally get a pause in the boot sequence where the checkdisk is run, with messages detailing progress, but all that happens is the error "unable to access the drive C" on each and every subsequent load.
Running checkdisk as you suggest from the recovery console works fine, no problems. Running it under windows without the Auto fix option works fine. The problem is that I can't get rid of the scheduled attempt which fails on every load.