Can you show your code?

Also you can try to disable Javascript in your browser and clear cookies and after that try to get file you need again (from the browser). If you get file than it's not Javascript problem (something wrong with you code)...

use strict;
use LWP::UserAgent;

my $ua = LWP::UserAgent->new;
#my $req = HTTP::Request->new(GET => 'http://search.cpan.org/CPAN/auth
+ors/id/G/GA/GAAS/libwww-perl-5.836.tar.gz');
my $req = HTTP::Request->new(GET => 'http://usename:password@host/path
+/to/file.zip');
my $res = $ua->request($req);

if ($res->is_success) {
    # here put what you want to do with the file
    # print $res->content;
    # or
    # open( my $file, '> file.zip');
    # print $file $res->content;
    # close($file);
} else {
    print STDERR $res->status_line;
}
[download]

a) are you trying to come up with a hack to be able to circumvent the mentioned problem (the site actaully points to some script or whatever that *afterwards* sends your browser the url to the file to download) in any given situation?

Then maybe just download whatever you get to a temp file- checkout the mimetype, if it's html/etc, reap it for a .zip url.

b) Or, are you trying to come up with a hack for this one site only?

Consider unix wget or curl instead. Do this in bash.