You need to slurp all of your data into a variable and use the /s modifier on your regex. You also need to be careful about how you are using your greedy matching. Finally, use backreferences to match the ending tags to the start tags. Here's how I might do it:

#!/usr/bin/perl -w
use strict;

undef $/;     # Slurp mode
$_ = <DATA>;

while (/<\?--([^-]*)-([^-]*)-->(.*?)<\/\?--\1-\2-->/sg) {
    print "1: ($1)\n";
    print "2: ($2)\n";
    print "3: ($3)\n";
}
__DATA__
<?--1-1-->
<b>This is option 1 ok</b>
</?--1-1-->
<?--1-2-->
<b>This is option 1 version b</b>
</?--1-2-->
<?--1-3-->
<b>Option 1 version 3</b>
</?--1-3-->
<?--1-Version4-->
<b>Option 1 version 4 Perl</b>
</?--1-Version4-->
[download]

-sauoq
"My two cents aren't worth a dime.";

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.