Another random hint: try submitting this form to a CGI script of your own design, one that will belch out the contents of the form.

#! /usr/bin/perl -t
use CGI qw/:all/;  #and strict, taint and warnings
print CGI::header;
use CGI::Carp qw/warningsToBrowser fatalsToBrowser/;

print "<ol>";
printf "<li>%s: %s " ,$_,  param( $_ ) for param;
print "</ol>";
[download]

It may very well be that you're just submitting the text "/tmp/hapmap/rs11581638_name.txt" in the field instead of the contents of the file... you may need to slurp the file and submit that  do{local $/; open $f,'>','/tmp/...';<$f>} or similar.

Ofcourse it's just a guess