mrbbking is right, we need more info from you. After seeing the solution for array from file and compare, i wonder if you need to chomp at least one of your arrays first.

jeffa

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
F--F--F--F--F--F--F--F--
(the triplet paradiddle)