PHP max_execution_time Limits

Using PHP 5.3.3 via FCGId, I have:

Server Configuration>Website Options>Maximum PHP script run time = 180.

Services>PHP 5 Configuration>Resource Limits (/home/vhost/etc/php5/php.ini)>Maximum execution time = 90.

A valid and working .user.ini with "max_execution_time = 180" inside a subdirectory of my vhost (where phpmyadmin is installed). I know the .user.ini is working because phpmyadmin correctly reports to overriden value for upload_max_filesize.

php-info running in this subdirectory shows max_execution_time local = 180, but the max_execution_time master = 90.

What do I have wrong? I want max_execution_time = 180 only for phpmyadmin.

Thanks