It's hard to guess. Perhaps either open filehandle counts or locked memory. CGI.pm will load as much of the file as possible into memory (whatever is currently available to a fh->read call) so that might impact your locked memory usage. While I'm no OS programmer I always thought that memory was locked so you do an immediate read/write from it - perhaps you're tying up valuable space with your data. I also spent a minute reading each of your imports to guess at the number of open file handles (not much but perhaps more than you expected) to see if that was the problem.

Counting file handles: low teens.

1 perl
1 the script
1 DynaLoader.so / .dll
3 CGI.pm
=> Carp.pm
=> Exporter.pm
2 Fcntl.pm
=> Fcntl.so / .dll
1 File/Basename.pm
? I don't know whether to count STDIN/STDOUT.
1 The file opened on disk for storing the uploaded file.

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