You reuse the variable $key and I think it might be confusing things for you. The if in your foreach loop will always be true because $key comes from keys in %hash.

while (<$in1>) {
  chomp;
  my ($key1,$value1) = split (/\s*=\s*);
  if defined($hash{$key1}) {
     print "$key1 is in both!\n"
  }
}
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