Goodness, I like perl. Here's the same thing in a fraction of the lines. It probably works.

use List::Util 'max';
use File::Copy 'copy';
use File::Slurp qw'read_file write_file';

@ARGV == 1 or die "$^X $0 filename.pl\n";
my $file = shift;
copy $file, "$file.bak"
    or die "Couldn't copy $file to $file.bak: $!";
my $source = read_file( $file );

$source =~
    s(^#/*.*\n((?s:.+?))^#*/.*\n){
        my @lines = map /^\s*#\s*(.+?)[\s#]*$/, split /\n/, $1;
        my $len = 1 + max( map length(), @lines );

        join "\n",
            "#" x $len,
            map( sprintf("%-" . ($len - 1) . "s #"), @lines ),
            "#" x $len
    }meg
    and write_file( $file, $source )
    or die "Couldn't write changed source to $file: $!";
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