Drush not using drush.ini

I'm working on a remote CentOS server with full root access.
Only started using Drush a few months ago and am addicted now. It was working fine for downloading and installing Drupal & modules and a few other things.

Just recently, our server person had to harden server (we had a security breach, it was unrelated to Drush or Drupal) and Drush isn't working any more:

root@server [~]# drush st
exec() has been disabled for security reasons environment.inc:689 [warning]
The following restricted PHP modes have non-empty values: [error]
disable_functions. This configuration is incompatible with drush.
Please check your configuration settings in /usr/local/lib/php.ini or
in your drush.ini file; see examples/example.drush.ini for details.
exec() has been disabled for security reasons environment.inc:689 [warning]
PHP configuration : /usr/local/lib/php.ini
Drush version : 4.5
Drush configuration :
Drush alias files :

Ok so the first thing is to override the .ini file for drush so I can get rid of disable_functions.
I do have rights to edit the server's main php.ini file directly, but that kind of defeats the security changes, so I'm trying to do this the "right" way:

1. Copied a modified version of /usr/local/lib/php.ini to /usr/local/lib/php/drush
2. Restarted my SSH session
3. Invoked drush st again

The output is identical - the PHP configuration shows that the new ini file isn't being picked up, and I'm getting the same disable functions error.

I then tried:
1. Created new directory /home/.drush and copied a modified version of the /usr/local/lib/php.ini file there.
2. Restarted my SSH session
3. Invoked drush st again

Same result.

I've followed Drush's readme instructions on overriding the .ini, and become closer friends with google, but no joy yet. I'm a developer, not that experienced with servers, and our server person knows nothing of drush, so if someone can point me in the right direction on this I'd appreciate it.

Mike
Republic of Ireland