Changing the order to the following seemed to resolve the issue.

httrack <http://www.empiremediationservices.com/> -c1R2Kb1s0ap0r3F  "HTTrack
cache
builder" -*.jpg -*.css -*.js -*.png -*.gif -*.jpeg -*.ico -F
"Mozilla/4.0 (compatible; MSIE 6.0; Windows CE; IEMobile 7.11"