A friend tried this and doesn't seem to see the problem.  The main difference is that he is testing with Apache 1.3 whereas I was testing with Apache 2... perhaps that is the key somehow?  I will try to test it myself when I have time but I thought it might click for someone so I'm noting it now.

Please add a short example script which shows the problem
clearly.

Ok... you need 2 files.

--------------file1.php-----------------------
<?php
require 'file2.php';

function f2($param) {
	f3($param);
}

function f1($param) {
	f2($param);
}

f1('foo');
?>
----------end file1.php---------------

----------file2.php---------------
<?php

function f3($param) {
	echo '<table border="1">';

	$backtrace = debug_backtrace();

	foreach ( $backtrace as $frame ) {
		echo "<tr><td>$frame[file]</td><td>$frame[line]</td><td>$frame[function]</td><td>";
		print_r($frame['args']);
		echo "</td></tr>\n";
	}

	echo '</table>';
}
?>
-------------end file2.php---------------

On my server (apache2, php4.3) I get:
/home/julian/public_html/file1.php 5 f3 Array ( [0] => foo )  
/home/julian/public_html/file1.php 9 f2  
/home/julian/public_html/file1.php 12 f1  

But on my friend's server (apache1.3, php4.3) - though there are surely plenty of other differences as well - I get:
/web/sites/Julian/docs/file1.php 5 f3 Array ( [0] => foo )  
/web/sites/Julian/docs/file1.php 9 f2 Array ( [0] => foo )  
/web/sites/Julian/docs/file1.php 12 f1 Array ( [0] => foo )

This worked for me with both PHP/CLI and under Apache2 just fine..

How did you configure PHP and Apache2?
What MPM is Apache2 running as?
Which Apache2 version?

Aha!

Trying it with the CLI inspired me.  I tried it myself and still had problems, but that eliminated apache2 as the problem.  Then I realized I had Zend Optimizer enabled and that proved to be the problem -disabling Optimizer makes it work properly.  I guess that makes a certain amount of sense.

Do you have any idea if that would be considered a bug in Optimizer or if it's just an unavoidable problem?

Definately optimizer bug. You need to report that to Zend..