Sorry, I may be missing something here but isn't your rewrite rule rewriting everything to be on the end of index.php anyway?
i.e. by typing http://host/index.php/blahblahblah you're effectively writing http://host/index.phpindex.php/blahblahblah? Have you tried without the index.php in your url?
Yeah, I think you're right, I just tried putting index.php into my location bar like you and it still worked (I also use virtual hosting).
If I were you, (based on the info you've given me) I'd try and rewrite my virtualhost section in my http conf file. Comment out your old virtualhost rules (including filesmatch) and try something like:
If it works then try building on it your old rules until something stops working. If that doesn't work... well I'm sure someone else with a better idea than me can help out... ;)
I'm short of knowledge on this, but I had experienced the same problem a week ago, there is a patch for EZP on PHP-CGI setup at http://www.ez.no/developer/ez_publish_3/forum/install_configuration/my_final_patch_for_phpcgi
I have applied with success, but now I have another issue regarding the URL format and the performance of the installation