Dear Gwyn-Evans,
To make sure that the change was correctly applied, create a file called test.php with this content in it:
<?php phpinfo(); ?>
Upload to the root folder of your wordpress and view it with your web browser: http://www.yousite.com/test.php
Here you can verify that max_input_vars, suhosin.post.max_vars and suhosin.request.max_vars have all been increased to 3000.
Let me know if this is all correct.
Regards,
Caridad