Interesting; I am unfamiliar withe the file handling mechanism you use; while I would love to advise you on that, I'll leave that to others.

Here is a snippet showing how I do my file uploads:

      my $inpfsz = 0; 
      open(RESFIL, ">$desfnm"); 
      binmode(RESFIL); 

      while (my $inpcnt=read($srcfnm,$inpbuf,2096)) { 
            $inpfsz += $inpcnt; 
            print RESFIL $inpbuf; 
      } 

      close(RESFIL);
[download]

You can find more detail, including some mandatory advice about the HTML that drives the upload, at http://www.bhmk.com/mariners/cspupld.htm.