The critical point to remember is that
    $rgb[16]=pack("S", 7360);  # Overwrite 3689 with 7360
does not assign 7360 to  $rgb[16] but instead assigns a two-byte string that is the S-packed representation of 7360. After the pair of assignments in your OPed code,  @rgb contains a Hellish mix of numbers and strings. Don't do that. Instead, just assign numbers to the array elements and re-pack:

c:\@Work\Perl>perl -wMstrict -MData::Dump -le
"my @ra  = (1, 3689, 2, 2462, 3);
 dd \@ra;
 ;;
 my $pS1 = pack 'S*', @ra;
 dd $pS1;
 print 'length $pS1 == ', length $pS1;
 ;;
 my @rb = unpack 'S*', $pS1;
 dd \@rb;
 ;;
 $rb[1] = 7360;
 $rb[3] = 4912;
 my $pS2 = pack 'S*', @rb;
 dd $pS2;
 print 'length $pS2 == ', length $pS2;
 ;;
 my @rc = unpack 'S*', $pS2;
 dd \@rc;
"
[1, 3689, 2, 2462, 3]

"\1\0i\16\2\0\x9E\t\3\0"

length $pS1 == 10
[1, 3689, 2, 2462, 3]

"\1\0\xC0\34\2\x000\23\3\0"

length $pS2 == 10
[1, 7360, 2, 4912, 3]
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