The files are uploading fine but I'm not getting the values of the hidden fields.

It makes absolutely no difference if you're uploading a file at the same time or not.

#!/usr/bin/perl

use strict;
use warnings;

use CGI;

my $cgi = CGI->new();

print $cgi->header('text/plain');

print('URL=', $cgi->param('URL'), "\n");
print('Alias=', $cgi->param('Alias'), "\n");

my $fh = $cgi->param('FILE');
print("--\n");
print while <$fh>;
[download]

One thing should verify is that you actually gave a value to the hidden fields.