Thanks jsprat (and dws -- I should have tried Deparse). I do believe we have a bug, but I got a feeling it's already been reported(will search). Anyway, here is a simpler example that I might submit as a bug report (and I hope this is easy enough to follow BrowserUk).

## in the substitution part (the second half),
## the /\[B\]/ is turned into /[B]/, see results
## and deparse output at the end
my $t  = '[A] yoda [B] jeffa [C]';
$t =~ s
    {
        \[A\]
        (.*?)
        \[C\]
    }
    [
        my $r = $1;
        if( $r =~ /\[B\]/ ){
            $r =~ s/\[B\]/GOT B/;
        }
        $r;
    ]gsex;

my $o  = '[A] yoda [B] jeffa [C]';
$o =~ s
    {
        \[A\]
        (.*?)
        \[C\]
    }
    {
        my $r = $1;
        if( $r =~ /\[B\]/ ){
            $r =~ s/\[B\]/GOT B/;
        }
        $r;
    }gsex;

# happens here also, but is not significant
# since <> aren't metacharacters
my $p  = '<A> yoda <B> jeffa <C>';
$p =~ s
    {
        \<A\>
        (.*?)
        \<C\>
    }
    <
        my $r = $1;
        if( $r =~ /\<B\>/ ){
            $r =~ s/\<B\>/GOT B/;
        }
        $r;
    >gsex;

print "
$t
$o
$p
";
__END__

 yoda [GOT B] jeffa
 yoda GOT B jeffa
 yoda GOT B jeffa

# -MO=Deparse output
my $t = '[A] yoda [B] jeffa [C]';
$t =~ s[\n        \[A\]\n        (.*?)\n        \[C\]\n    ][my $r = $
+1;
if ($r =~ /[B]/) {
    $r =~ s/[B]/GOT B/;
}
$r;]egsx;
my $o = '[A] yoda [B] jeffa [C]';
$o =~ s[\n        \[A\]\n        (.*?)\n        \[C\]\n    ][my $r = $
+1;
if ($r =~ /\[B\]/) {
    $r =~ s/\[B\]/GOT B/;
}
$r;]egsx;
my $p = '<A> yoda <B> jeffa <C>';
$p =~ s[\n        <A>\n        (.*?)\n        <C>\n    ][my $r = $1;
if ($r =~ /<B>/) {
    $r =~ s/<B>/GOT B/;
}
$r;]egsx;
print "\n$t\n$o\n$p\n";
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