When I experience such weirdness I turn to Corion's fantastic WWW::Mechanize::Shell:

>perl -MWWW::Mechanize::Shell -eshell
(no url)>get http://genie.dartmouth.edu/scope/
Retrieving http://genie.dartmouth.edu/scope/(200)
http://genie.dartmouth.edu/scope/>dump
POST http://genie.dartmouth.edu/scope/startscope.php (multipart/form-d
+ata) [paramForm]
  paramFile=none                 (hidden readonly)
  upstream=none                  (hidden readonly)
  runBeam=Yes                    (hidden readonly)
  runAmbiguizer=Yes              (hidden readonly)
  runBipartites=Yes              (hidden readonly)
  upstreamType=intergenic        (radio)    [*intergenic/Intergenic|fi
+xed/Fixed]
  group=                         (textarea)
  groupFile=                     (file)
  emailAddress=                  (text)
  emailSubject=                  (text)
  selectParamsButton=Run SCOPE   (submit)
[download]

Gadzooks, no 'species' input in sight, or any other select option! Comparing the Source html to the values we can see via WWW::Mechanize::Shell I would think that since there are no option tags we can't use them as a valid input. They seem to be using JavaScript to populate the options for the select boxes. <joke>Insert anti JavaScript comment here :P </joke>.

WWW::Mechanize does not support JavaScript, When using Firefox with NoScript none of the select boxes have any options, I strongly suspect that this is the problem you face. Why not try automating your browser (via Mozilla::Mechanize or Win32::IE::Mechanize or alike) which does understand JavaScript to achieve your goal.

Hope this helps

Update: Added the sentence "They seem to be using JavaScript to populate the options for the select boxes." for clarity

Martin