|if i understand you correctly your trying to run chkdsk to 100% via using the recovery console on the vista install cd. hoping that this will then allow you to be able to run it on your pc later on and it not freeze.|
first a few questions:
have you tried running it in safe mode?
or initiating it via command prompt/ right click on the drive?
is this on your primary drive? (as which it should run on a restart and not during your windows session)?
have you really left it long enough? (it can appear to hang on a stage, i once had to leave it running all night)
First off youll need your vista install cd to be able to run chkdsk from its recovery console.
this link explains it well, what you want is method two.
Vista Forums - chkdsk