I've just upgraded from php 4.02 to 4.04 using PHPTriad, and have experienced exactly the same problem. So all I'm doing here is adding to your cry for help. So, if you (Andreas) have found the solution since - please let me know.
I'm only trying to include other scripts from the very same directory, eg.
include "foo.php"
This used to work fine, and now it doesn't. The exact error message looks like this:
Warning: Failed opening 'footer.inc' for inclusion (include_path='\apache\includes;\apache\htdocs\;\apache\htdocs\phpmyadmin') in c:\apache\htdocs\fpc.wa.gov.au\www\admin\index.php on line 8
Thanks for any help.