Clearly, the nature of the script could have some impact, and the OS is likely to be responsible for some small variance in compile speed, but it seems likely, at first glance, that the issue is the capabilities/resources of the processor in each box. You've hinted as much with your contrast between the two, where the Linus machine is

"a pretty high powered workhorse, compared to the Windows server"

Of course, it would help to know more specifics: what version of Linux and of Win server, what are the characteristics (processor, RAM, drive(s)) of each machine and which version of Perl is resident on each machine?