You may have to apply some kind of recursive script in .htaccess at the MODX install directory. (my host does this)
Example:
<IfModule mod_suphp.c>
suPHP_ConfigPath /home/username/php.ini
<Files php.ini>
order allow,deny
deny from all
</Files>
</IfModule>
Also, because I upgraded php I have to include this in my .htaccess. Prior to adding the following, my php.ini had settings that were correct, php.info said they were correct, but I got errors that said they weren't.
# Use PHP 5.3
AddType application/x-httpd-php53 .php
My point would be that somehow there's a conflict between php.ini and what settings are actually being used (not that the above code will solve your problem, they are just examples of things I've had to change). PHP documentation at your host might clue you in as to why.