Hi Peter,
Not much on Windows script command programming, but I can tell you that running Chkdsk on startup can be tricky. It first of all needs to be run in an Administrator level CMD prompt or in a SAFE MODE configuration. Chkdsk no longer runs in Standard Mode to completion on most Windows computers Vista and later due to Anti-Virus/Anti-Spyware being loaded in front of Chkdsk command and especially if your AV or AS security software is checking for Rootkits. Not sure why you want to run this, as checking for and clearing bad sectors on bootup is a thing of the past; even more so from what I understand about SSD drives work if you are using one of those with your intended command script.
Sorry that's not much help, but, what...