This one took us a bit to figure out
In th admin interface, go to "External Apps" and then edit the one for your PHP. Look a the "command" line. On the command I believe there is a -c (it's been removed from ours so I can't tell you the exact parm). That is overriding the compiled part for the php.ini. Just remove the -c and the path, save and restart and you'll start using the compiled path for php.ini.
Frank