you have your params mixed up.  replace arg_separator.output
with arg_separator.input and things will work.  I modified
your script below.  This one works as you wanted it to.

<?php
global $HTTP_POST_VARS,$HTTP_GET_VARS, $HTTP_COOKIE_VARS,
$PHP_SELF;

ini_set("arg_separator.input", ";");
define("a", ini_get("arg_separator.input"));


if($HTTP_GET_VARS){
$total = count($HTTP_GET_VARS);
echo "Displaying GET variables";
while(list($key, $val) = each($HTTP_GET_VARS)) {
echo "<br />Key: '$key'   Value '$val'";
}
}


echo "<hr>";
echo "<A HREF=\"$PHP_SELF?i=am".a."do=one\">Click to
activate test</a>";
echo "<hr>";

?>

i have gotten emails from people saying that they have reproduced
this error.  Can anybody from PHP verify this?  I have not been
able to reproduce this error (using the script in my last post.)

ok...  the problem exists in your script at

http://wart.phpking.org/test.php

but using the EXACT script that I created, it works fine...

Please use this one... (EXACTLY)

status -> closed

This is a tricky lil bug, real easy to overlook. At the following url i have a script with your example code - and it does not function properly:
http://wart.phpking.org/test3.php

you can see some other examples of how this doesnt work at
http://wart.phpking.org/test.php
http://wart.phpking.org/test2.php

again, this seems to execute fine on windows based php/apache systems
(which is probably a good clue as to where the problem exists).

- ini_get("arg_separator.input") does not return the 'local' value, but instead the default or php.ini value (this is different than with ini_get(
"arg_separator.output"). Perhpas this is intensional?

- the above problem probably contributes to the fact that where the query_string is parsed for variables - it always gets the default arg_separator.*

arg_separator.output - defines which separator character
is used in the PHP written URLs (ie. transparent sessids)

arg_separator.input - defines which separator characrters
(yes, there can be many) are used to separate the variables
in query string. This can NOT changed in script since
the time the script is run, the query string has already
been processed. You can only change this in php.ini / httpd.conf / .htaccess files.

Reclassified as documentation problem. The ini-directives
documentation lacks (not only) these. Also, the documentation should be restructured to show which directives can be change and where. Some kind of table maybe?

--Jani

We already have a nice and up-to-date table with all ini options at http://php.net/manual/en/ini.php
Those particular options have already an explanation (which is linked from that table).