1. What program?

I'd look up a more specific answer such as I see at http://www.google.com/search?&q=0x80070725 but this information is missing in your post.

2. Use of MSCONFIG in SAFE MODE would be my first method.
http://www.google.com/search?&q=msconfig+extract+file

3. "As all us Windows ME users know, you simply cannot start Windows ME in MS-DOS mode... thanks Microsoft."

Which is why I use either a boot diskette or boot CD. You should set this up to recover from small disasters.
Available from:
http://www.bootdisk.com or
http://www.ultimatebootcd.com/

Bob