If I hold the first post as input, then your last post as correct output, I too get the expected output...

!/usr/bin/perl

use strict;
use warnings;
my $text;

while($text=<DATA>){
        $text =~ s~<font color=("|')?((\w|\s)+)("|')?>(.*?)<\/font>~\[
+color=$2\]$5\[/color\]~ig;
        print $text . "\n";
}

# expected output:
# [color=blue]<i><b> <br>Some text[/color],  <br>an a

__DATA__
<font color="blue"><i><b> <br>Some text</font>,  <br>an a
[download]

Yields:

[color=blue]<i><b> <br>Some text[/color],  <br>an a
[download]

Can you, maybe, explain in words? or have a larger sample set. Do you mean that this works, but when it is multi-line, then it doesn't match?