> (httrack
> -qir1%e0C2%PX0s0u1%s%uN0%I0p3DaK0c4H0%kf2A25000%f#f
> -F "Mozilla/4.5 (compatible; HTTrack 3.0x; Windows
> 98)" -%F "<!-- Mirrored from %s%s by HTTrack Website
> Copier/3.x [XR&CO'2007], %s -->" -%l "en, en, *" -%L
> C:oo0min_foo.txt -O1
> C:Inetpubwwwrootoooodiroodir)
> 
> It basically grabs a list of urls that is in a text
> file and updates the previously downloaded files.  I
> can paste the above command directly into the
> command line and it works.  However, when I try to
> run it from the .bat file, it doesn't work.  The log

Special to the shell are %, &, <, >.  Your &, <, and > are inside quotes so
they are ok.

httrack -qir1%e0C2%PX0... tries to substitute the variable e0c2.  Since that
doesn't exist you get:
httrack -qir1PX0... which doesn't work.  You need to quote the percents. 
Prefix each % with ^:
httrack -qir1^%e0C2^%PX0...