I abandoned the table. I've hard coded the logic into the loop and moved some of the work out of it.

#!/bin/perl5

use strict;
use warnings;

my ( @K_array, @R_array ) = ();
my $I = '';
my $out = qq(<c>\n);

while (my $l = <DATA>) {
  my ( $code, $value ) = $l =~ /^(\w|\#)\s+(.*)\n$/;
  $I = $value if $code eq 'I';
  if ( $code eq 'K' ){
    $out .= "<p></p>\n<t>\n" unless @K_array;
    push @K_array, $value
  }
  elsif ( $code eq 'R' ){
    $out .= "<r></r>\n" unless @R_array;
    push @R_array, "<li>$value</li>\n"
  }
  $out .= qq(<set name="temant">$value</set>\n) if $code eq 'S';
  $out .= qq(<setflag param="$value"/>\n)       if $code eq 'F';
  $out .= "<!-- $value -->\n"                   if $code eq '#'
}

my $K;
if ( $I ){
  $K = $K_array[0] # assumes only 1 K with I
}
else{
  $K .= '%' . $_ . ',' for @K_array;
  chop $K
}
$out =~ s|<p></p>|<p>$K</p>|;

my $R = join '', @R_array;
$out =~ s|<r></r>|<r>\n$R</r>|;
$out .= qq(</t>\n</c>);
if ( $I ){
  $out =~ s|<t>|<t>\n<ifflag param="$I">\n<then>|;
  $out =~ s|</r>|</then>\n</ifflag>\n</r>|;
}

print "$out\n";

__DATA__
C 1010
K Perl
K is
K cool
F 1234
S Alright
R Whatever
R More
R BlaBla
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