It would be logical that chomp isn't behaving the way you'd expect. Perhaps use regular expressions that explicitly state what you're trying to do until you're comfortable with how chomp functions. Or even write a function of your own.. e.g.

  sub remove_trailing_newlines( $ ) {
      my ( $stringref ) = @_;

      ${$stringref} =~ s/[\r\n]+\z//gs;
  }
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. Then call it instead of chomp. E.g.

  remove_trailing_newlines( \$cmd );
  remove_trailing_newlines( \$check );
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