The world of software optimization is a many headed beast. Your software may not even be the cause at all. There are literally hundreds of different things that could be causing your slowness. Here are what are most obvious to me to check:
What does your system look like when the scripts are being run? Running 'top' from the server, is it CPU locked, IO (disk) locked? Network locked?
What version of Perl (btw: its "Perl" not "PERL") are you running on the workstation? Is it the same threaded version of 5.8? If not, that might be your issue. The threaded Perl binary might be slowing you down. Don't think so though, but check it out.
How many people are running the script at one time? Obviously there are more people on the server than on your workstation.
Does it do any sort of database interaction that might be slowed down by table locks?
Those are a few things to check out.
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