Question - are your Linux boxes multicore as well? Are the perl programs using all of the cores on the Linux machines, or just bouncing from one to another?

Unless you have broken your data or code into parts that can be run in separate pieces, and then tell the OS / Perl to do that, it will not be done automatically. Most code, as written, will be compiled and run sequentially. It can be a black art to try to have the computer determine what can be paralellized.