Missing fields in query using Partner wsdl

I've been using the Enterprise WSDL for a while and am now switching to the Partner wsdl. I generated a new partner wsdl and copied it to my config.

But I'm missing fields in my query using the Partner WSDL. I originally created a php script that worked fine using the Enterprise wsdl, but once I switched to the Partner wsdl, several fields are missing from the query.

I have already verified that the fields and query are correct by copying and pasting the same exact query to the Force.com explorer and the custom field is definitely there. And -> Using "print_r" in php -> it's definitely *not* there. And iw *was* there when I was using the Enterprise wsdl. I'm being forced to migrate to the partner wsdl to obtain added functionality that we can't get using the Enterprise wsdl.

Is there some sort of API setting I need to set somewhere to see the custome field using the Partner wsdl?