That is because you have more than one bug in your code. As JavaFan pointed out your subroutine begins with

my(%site1)=@_;
my(%site2)=@_;
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which makes no sense as it will give you identical data in both variables. If you want to give two hashes to a subroutine you should use hash references instead, i.e.

sub x {
  my(%site1)= %{$_[0]};
  my(%site2)= %{$_[1]};
  ...
}

x(\%hash1,\%hash2);
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Also, as moritz repeatedly pointed out, you seem to have strings where you expected array references, so your data is different. So another bug is in the code outside of this subroutine

Please use Data::Dumper to check up on your data. For example add a line

  use Data::Dumper;
  print Dumper(\%site1);
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to your subroutine (and similar prints at other places) and compare your data structure with what you expect.