I’m also having similar issues with this site: <http://www.mmrjournal.org/>.
The page <http://www.mmrjournal.org/archive> has two drop-down menus that link
to journal volumes. In my scrape the volume 2 menu is dropped down and the
volume 1 menu doesn’t work; when I click on volume 2 it folds up and then
doesn’t work at all. 

Here are the parameters from the log file: 
HTTrack3.45-3+htsswf+htsjava launched on Fri, 18 Sep 2015 16:34:03 at -* 
+*.jpg  
+*.gif  
+*.css  
+*.js  
+*.png 
-*page2ad* 
-*google-analytics* 
-*paypal.com* 
-*akamaitech.com* 
-*google.com*  
-*doubleclick.com* 
-*googlesyndication* 
-*webtrendslive* 
-*sitemeter.com* 
-*ads.web.aol.com* 
-*nedstatbasic.net* 
-*webstats4u.com* 
-*webstats.motigo.com* 
-*statcounter.com* 
-*service.urchin.com* 
-*snap.com* 
-*stats.wordpress.com* 
-*visit.webhosting.yahoo.com* 
-*mailto* 
 +www.mmrjournal.org/* www.mmrjournal.org/ 
(httrack -%F "<!-- this file was mirrored for the egranary digital library
from %s%s on %s -->" -F "mozilla [en] egranary digital library system" -Q -C2
-t -%P -n -s0 -%s -%u -N0 -p3 -D -a -K5 -H0 -%k -f2 -A25000 -%A
cgi,php,php3,asp=text/html -%f0 -#f -q -X -#L -o0 -u2 -O
X:\egRawScraped\www.mmrjournal.org,X:\egCache\www.mmrjournal.org -%S
X:\UpdateSW\HTTrackScanRules\ScanRulesFull.txt +www.mmrjournal.org/*
www.mmrjournal.org/ )