You'd be better off investigating the new options of chkdsk that make the boot time run unnecessary.

Its not totally unnecessary

No big deal. You have a small boot disk that is hardly ever going to change, so won't need to be checked and is unlikely to get corrupted. Then you use the more resiliant file system for volumes that are going to change frequently. It's a classic way of installing an operating system.

In reply to a post by MrTAToad2:

Shame that Windows can't be booted off it...

It is, indeed, a shame it can't be booted from yet, but NTFS is a wonderful filesystem and incredibly resilient against any sort of logical corruption or otherwise. Unless you are in a rescue situation the /R is totally pointless, if you are in the situation where you need to be running /R on a hard disk you should be running it from another volume or boot media, ideally via cmd, not from the Windows boot process. If you have a single bad sector that is bubbling up to the OS/application layer - it is time to bin the HDD, the /R is last resort to salvage the integrity of the filesystem without resorting to data recovery.

That would be true if I had a faulty hard drive.

If you don't have a faulty hard drive, there is no need to run chkdsk with /r .

You don't even need to run chkdsk with the /R option to find out if it has bad sectors - just check SMART data, this will detect and correct bad sectors well before Windows knows about them.

This post wasn't to discuss whether or not it should be run - perhaps re-reading my original post may help to refresh your memory about what the post was about...

I seem to recall when running the /R option the progress status has always been a bit inaccurate, even in Windows 95 it took ages and was hard to calculate when it would finish? If I ever run an /R I expect 12-24hrs downtime..

You would think they would be able to calculate percentages correctly, after all these years...

Probably wouldn't take much code to figure out how many sectors are being scanned, and get a ETA using total sectors, but I think Microsoft would tell you its not worth the time coding this in.