[Php-java-bridge-users] Certs, security & general configuration question

Figured something out today.
Seems my app will run in a console (via #!/bin/env php) with no hiccups.
Now if i take the exact same php code and try run it through apache, then i
get the problem mentioned (check first post to this thread).
This leads me to believe that apache doesn't have rights to access certain
paths on my box.
Could someone point me in the right direction, i think i have to setup
apache differently to access my java installed certs and other security
files...