Why are you using sed when you can use Perl directly?

open my $fh1, '<', "file1"
    or die "Couldn't read 'file1': $!";
my %delete = map { s/\s*$//; $_ => 1 } <$fh1>;

open my $fh2, '<', "file2"
    or die "Couldn't read 'file2': $!";
while( <$fh2>) {
    my( $key, $value ) = split /\s*=/;
    if( ! $delete{ $key }) {
        print $_;
    } else {
        # skip this key
    };
};
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If you want to keep on using sed, my advice is to print all the commands you're launching and then inspecting them or running them from the command line separately.