Edit: Can't write quick enough! You were correct, I think I was trying to use the string itself as its place in the array. Your example is easier to follow than my workaround so I'll try that. Thanks!

I did show it, albeit it was inline with other text so easy to miss.

if($lines1[$_] eq $lines2[$_])

I have fixed it by creating a basic for loop and iterating through using the size of the array as the limit. Which now seems to work:

for(my $i = 0; $i < @lines1; $i++) {
   if($lines1[$i] eq $lines2[$i]) {
      print("same.\n");
   } else {
      $difference++;
}
[download]

That seems a bit archaic and far too long to be Perl, but I wrote it and it works so I'm happy to use it!