Permission errors when creating a PDF

When I attempt to create a PDF using PHP's exec() I get a lot of the following errors, and no PDF file is created.

shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied
job-working-directory: error retrieving current directory: getcwd: cannot access parent directories: Permission denied
job-working-directory: error retrieving current directory: getcwd: cannot access parent directories: Permission denied
chdir: error retrieving current directory: getcwd: cannot access parent directories: Permission denied

I've tried changing permissions on the directory to 777 and have tried switching the owner to the PHP user but still nothing. Now when I run the same command in Terminal on my mac, it works great and the PDF is created.

Is there anyway to debug this more? Any ideas on what I can try to fix these permission errors?