What compression tool are you using?

Even if that tool doesn't have a batch/command-line way to run it, there are probably other equivalent tools out there. For example, you might look at http://multivalent.sourceforge.net/Tools/pdf/Compress.html It is admittedly not in perl (it is in the other popular four-letter cross-platform language), but it is a free tool that shrinks PDF files but keeps them as PDF format (i.e. it does the compression internal to the PDF format so they are directly readable by PDF viewers). It is command-line based. There is a perl script up on http://wiki.scribus.net/index.php/Web_optimised_PDF that uses the ghostscript library to create smaller PDF files -- that particular script is from a package called "Scribus", but it could serve as a starting point).

Best of luck.