When performing a CHKDSK from Live connect or a "execute shell command" Via a script results in errors being found. When run form the machine its self No errors are found.
When CHKDSK is run in a 32 bit environment on a 64 bit machine errors will be found.
For live connect there is no workaround.
For agent procedures ensure you're executing the script in 64 bit mode on 64 bit machines.