Personally I set up $ENV{PATH} so that it only contains either C:\strawberry\perl\bin or C:\strawberry-5.8.8\perl\bin (a renamed older directory) or C:\Program Files\Perl\bin, but the general approach of using different directories for different installations of Perl is a sane approach.

I'm not sure why people find difficulties there, or what difficulties they encounter, but then, I presume that to most of the people writing such guides, or maintaining Padre, Windows is a foreign system and they believe that there are demons everywhere to devour them.