Use of uninit val in concat (.) or string at filebot.pl line 149.
Use of uninit val in subst (s///) at filebot.pl line 150.
Cannot do that because Is a directory at filebot.pl line 157.
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That's 2 warnings and 1 error. The warnings might not amount to anything, but something tells me that this line:

$file =~ s/.*[\/\\](.*)/$1/gi;
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is going to break ... use File::Basename instead.

The error is one of these two die's:

sysopen( ... ) or die "Cannot do that because $!";
...
   print UPLOADFILE or die "Cannot do that because $!";
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and i'd put my money on the first one. Make absolutely sure that the web server can create files in the directory and make sure that the file doesn't already exist (or take out O_EXCL from the sysopen call). You might also want to make sure that uploaded file handle is valid as well:

die "not a Fh" unless ref($upload_filehandle) eq 'Fh';
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