You cannot manipulate the php.ini settings with .htaccess when running php as cgi/phpsuexec.
If you are using .htaccess with php_ value_entries within it, you will receive an internal server 500 error when attempting to access the scripts.
This is because php is no longer running as an apache module and apache will not know how to handle those directives any longer.
Check that the php script you are attempting to execute has MAXIMUM permissions of 755. (644 will work just fine normally.)
If your script has permission of 777, then it will generate a script error 500 message.
Check that the directory permissions that the script resides within is set to a MAXIMUM of 755. This also includes directories that the script would need to have access to.