I had the same problem. This is what worked for me:
My host runs Suphp on my server:
Remove all php commands from .htaccess
Put:
suPHP_ConfigPath /home/yoursite/public_html/
in your .htaccess file (at the very top).
Cron Jobs:
***** /usr/bin/php -c /home/yoursite/public_html/ -q /home/yoursite/public_html/periodic/cron.php
The above is what my host suggested and it works.
Creat a php.ini file in the root of your D7 install
and put:
allow_url_include = off
you can get a sample php.ini file off the net - search google.
You do not need to put a php.ini file in any other directory for this to work.
There are none so blind as those that will not see.