First, please put your code inside <c></c> tags to make it easier for others to read. (For an example, see the code in this post.)

Second, can you specify which array(s) you believe to go out of scope and share what kind of error/warning messages you are getting? Without this information, it makes it a bit challenging to figure out which of the several arrays you're having problems with. Since you're using both strict and warnings, you should be getting some useful error/warning messages that will help in debugging the code.

Also, I believe that the last little bit of code at the end of your post has some incorrect syntax. It probably should be rewritten to be more like the untested code below.

use warnings;
use strict;

my $equals = 1;
for (my $i=0;$i<$#array1;$i++) {
  if ($array1[$i] ne $array2[$i]) {$equals = 0;}
  else {$equals = 1;}
  print $equals;
}
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Of course someone more familiar with the ternary operator than I am will probably point out that the if statement can be shortened to a single line. I think it's would be something like: