The standard Perl references,
Learning Perl
Programming Perl
Advanced Perl Programming
The Perl Cookbook
were written before Activestate really got going, and/or have a slight bias toward Unix implementations. Linux is a Posix or Unix clone. Other great Perl books also have this bias. Unix was Perl's main platform for some time.

There is Learning Perl on Win32 Systems which I would get were I using Perl on Win32.

99.5 percent of what you do will be the same. As one who endeavored to learn, alone in the wilds, K&R C on Xenix from mostly CPM orientated references; I will point out that tripping over that half percent can be a hard fall. Use the operating system of your choice.

Having the right documentation makes all the difference.

You might surmise that I like books.