You're not using binmode() on $upload_filehandle, though. You want to make sure you read in binary mode, too.
As for file size, if you have binary data in the input file but it's not in binary mode, you could have issues there.
Also, make sure you have a version of CGI.pm that doesn't have the fairly recent broken upload problem. CGI 3.21 and 3.22 simply don't work for uploads. See Skip CGI.pm versions 3.21 and 3.22 when upgrading -- they break the upload() method for more info. It could be you're not getting a file uploaded because the library really is broken.
What does print $CGI::VERSION; give you?
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