Thanks for the upload() tip. I found an example here at the monastery and plugged it into my code. Worked wonderfully.

Here's my revised code:

$| = 1;
my ($file,$path) = @_;
my $filename = $query->upload($file);
my $buffer;

open(OUTPUT, ">$path/$filename"); 
binmode($filename);
binmode(OUTPUT);

while( read($filename, $buffer, 64*2**10) ) {
    print OUTPUT $buffer;
}

close(OUTPUT);
return ($filename);
[download]

I would still like to know what the original problem was, but right now I just need a solution.