We experienced the problem you mentioned and spent hours fixing the problem.
What you have to do is add the line :-
Action application/x-httpd-php3 /path/to/php
underneath the part in the php.ini where it says:-
AddType application/x-httpd-php3 .php3
AddType application/x-httpd-php3-source .phps
/path/to/php - is where the command line php program is stored.
Reboot apache and then everything should work.
Jason.