Falazar,
for what do you have the line :
use CGI qw(:standard);
in your code. You do not instantiate a cgi object, you do not use any of cgi.pm's objects functions. So I guess that you do not have a problem with cgi.pm but without :-) and your server could also simply deny file uploads. Did you check for that?

Have a nice day
All decision is left to your taste

Update
Well, you might better use a separate script to upload your files as Hero Zzyzzx provided one. While looking at yopur script I realized that you invoke your script to let it call itself in case someone wants to upload a file. That means to me that each time your script runs its running with a useless half of code :-). So better split em up into two scripts or just use the one if fileuploading is all you need.
But I highly recommend to you to go and to read Ovid's wonderfull Web Programming with Perl course. Thats a lot of good and interesting stuff about CGI (well, and Perl).
nuff said, enjoy your day :-)