if there is a way to tell it not to do such, I may have over looked it when reading through the man for it, please let me know

You want "cuddled else" (-ce):

perltidy -ce script.pl
[download]

The Perl Best Practices book recommends: "Don't cuddle an else". You need to buy the book if you want to know the reason. Perhaps perltidy adheres to this as its default behavior.