I looked again at this thread and at kcott's line by line solution at Re: Removing multiple trailing comment lines from a string
I would also be thinking of parsing line by line instead of as string.
I've shown another method for that.

Some general comments re: .ini files:

• I find the comments meaningless unless I have to modify and re-write the .ini file.
• These kind of files often are a mixture of program generated and user modified contents.
  The comments can be very helpful to the user although they are meaningless to the program. I am unsure that modifiying the user typed in comments in any way is a good idea? Mileage varies.
• Getting a definition of what the file looks like exactly is in my opinion important.
• Some files have an important "root" un-named section at the beginning with maybe version number and stuff like that as well as sometimes parameters which over-ride variables with the sections. Whoa! If you are writing or can influence the spec, I would recommend not doing that.
• Some Perl modules like Config Tiny do a good job at getting the basic parms into an HoH. Something this code does not handle (nor others)

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my %HoA; 

while (my $line=<DATA>)
{
   my $next_line = process_section ($1) if $line =~ /\s*\[\s*(\S+)\s*\
+]/;
   if (defined $next_line) {$line = $next_line; redo}
}

print Dumper \%HoA;

sub process_section
{
   my $section = shift;
   my $line;
   
   while (defined ($line=<DATA>) and $line !~ /\s*\[\s*(\S+)\s*\]/)
   {
      chomp $line;
      next if $line =~ /^\s*$/; # skip blank lines
      push @{$HoA{$section}}, $line;
   }
   
   # delete the "trailing comments" in this [section] heading
   
   my $comment;
   while ($comment = pop @{$HoA{$section}} and $comment =~ /^\s*;/ ){}
+;
   push @{$HoA{$section}}, $comment;
   
   return $line;
}

=prints
$VAR1 = {
          'AnotherSection' => [
                                '; another comment',
                                'asfld=69'
                              ],
          'MySection' => [
                           '; This is a comment line for MySection',
                           'fld1 = \'value of field 1\' ',
                           'fld2 = 42'
                         ],
          'WhitespaceSection' => [
                                   '    ; Comment starting with a tab'
+,
                                   '     ; Comment starting with a tab
+ and a space',
                                   ' ; Comment starting with a space',
                                   '; Comment ending with a tab ',
                                   '; Comment ending with a tab and a 
+space  ',
                                   '; Comment ending with a space ',
                                   '     ; tab+space+comment+space+tab
+  ',
                                   '    ; space+tab+comment+tab+space 
+   ',
                                   'qwe=rty',
                                   'asd=fgh'
                                 ]
        };

=cut



__DATA__
; this is root section
a = 2
; some comment in root
b = 3
; some trailing comment in root
[MySection]
; This is a comment line for MySection
fld1 = 'value of field 1' 
fld2 = 42

; This is the heading for AnotherSection
[AnotherSection]
; another comment
asfld=69

 ; Heading for WhitespaceSection
[WhitespaceSection]
    ; Comment starting with a tab
     ; Comment starting with a tab and a space
 ; Comment starting with a space
; Comment ending with a tab 
; Comment ending with a tab and a space  
; Comment ending with a space 
     ; tab+space+comment+space+tab  
    ; space+tab+comment+tab+space    

qwe=rty
asd=fgh
; trailing 1
    ; tab + trailing 2
 ; space + trailing 3
; trailing 4
[download]

PS: my previous code explicitly allowed more than 3 trailing comments because I thought that was a requirement and was one of the "problems". I am also not sure why some .ini file comments should be ignored and others not? That is a strange thing to me.