Maybe you should be working on the methods through an instance of CGI. This works for me: (with some more code in the midle, but this is the relevant part)

use CGI;

my $q = CGI->new;
my $fileHandle = $q->upload('file');
my $file = $q->param('file');

my ($buffer, $bytesread);
my $newfile = "/path/to/file";
open FILE, ">$newfile";

while($bytesread = read($fileHandle, $buffer, 1024)) {
        print FILE $buffer;
}   
close FILE;
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