I see that bundling is disabled as the default, thus the OP problem script should work as I see it.

update: Hm, when I use your configure 'bundling_values' the options should be case sensitive, but the original code has 'S=i' and when I execute:

  $ ./tst.pl -S4
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I get

  Unknown option: S4
  0
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There does seem to be a problem with how the module handles case when "bundling_values" is turned on...

When GetOptions is given 's=i' (lowercase) all works as expected:

Getopt::Long::Configure ("bundling_values");
my $myOpt = 0;
GetOptions('s=i'=> \$myOpt);
print "bundling_values\n";
print "$myOpt\n\n";

$ test.pl -S1
Unknown option: S1
bundling_values
0

$ test.pl -s1
bundling_values
1
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When GetOptions is given 'S=i' (uppercase) works opposite to expected:

Getopt::Long::Configure ("bundling_values");
my $myOpt = 0;
GetOptions('S=i'=> \$myOpt);
print "bundling_values\n";
print"$myOpt\n\n";

$ test.pl -S1
Unknown option: S1
bundling_values
0

$ test.pl -s1
bundling_values
1
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Workaround by adding 'ignorecase_always' option:

Getopt::Long::Configure ("bundling_values", "ignorecase_always");
my $myOpt = 0;
GetOptions('S=i'=> \$myOpt);
print "bundling_values, ignorecase_always\n";
print "$myOpt\n\n";

$ test.pl -S1
bundling_values, ignorecase_always
1

$ test.pl -s1
bundling_values, ignorecase_always
1
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