Hello, I have the same problems. 
I just installed php5.0-win32-200503170130.zip on IIS5 with Windows 2000 as ISAPI module and Per Directory Values does not work with some of the settings.
For instance, display_errors directive works fine, but register_globals DOES NOT.
The another problem is, phpinfo() output is not correct. When I set display_errors in the registry to a different value as in php.ini, in the output of phpinfo() the value of "local" column stays  untouched, even though the system reactions are like the new value was set.
The Version 5.0.3 has the same problems.

And Last But not Least: When I try to 

echo ini_get(<ini_directive>);

,the value is correct as set in the registry, but the system does not work like it says- phpinfo() returns the old php.ini value and the system reacts as only the old php.ini was set.

This registry thing does NOT work for any option.
It's just before script execution so it techinally can't work with e.g. register_globals.

It read point needs to be adjusted then so it can work for register_globals.  I don't want to for register_globals on for everyone just because a couple of my customers have older scripts that like it.

I also don't understand why this is such a problem since the Apache module can do it with a .htaccess file.  In a practicle since, I don't see a difference between the .htaccess file in apache and the registry in IIS.

Sniper@php.net, i am sorry, what is your point? I was setting up different servers last week, with Apache and .htaccess there was not any problem. Just because these scripts have to be at the IIS, I do not come around it. I thought the sense of Per Directory Values Windows Registry paradigm was reading out the registry at the starting point of IIS, and setting local values for some directories, for specific configuration settings.
According to http://de3.php.net/manual/en/ini.php#ini.list register_globals is of type PHP_INI_PERDIR, which actually means you can set it locally. Moreover, with Apache1.3 and Apache2.0 this actually WORKS! So what's wrong with the Windows implementation?
I would not turn my scripts to register_globals on, but just as jsonger I have some external scripts running on this server. Thats why I want to have php.ini set to register_globals off and turn it on just for the foreign scripts...

Documented for now in XML sources.