I just tried logging in to http://www.pharmgkb.org/mypharmgkb/index.jsp which is presumably what you're trying to do?

I don't have a username and password, but this code worked just fine (it gave me an error because it's an HTTPS form action and I don't have the right module, but it definitely didn't submit the search form):

use WWW::Mechanize;

my $agent = WWW::Mechanize->new();
$agent->get('http://www.pharmgkb.org/mypharmgkb/index.jsp');
$agent->form(2);
$agent->field('username','perlmonk');
$agent->field('password','knomlrep');
$agent->submit();
[download]

Obviously my code's slightly different to yours, but I'm baffled as to how you've submitted the other form.