I'm trying to query for information using the PHP API (v20) and I am unable to query any custom object fields. The only one that appears to work is Id. It gives no error, in fact, the query itself works. It only returns the Id, whether or not I queried for it. Though, if I had not queried for it then the Id field is blank.
The following is a sample of what I get back from a query. I tried updating the enterprise.wsdl.xml to one tailored to my Org, but it still doesn't work. Is there something I am missing? I'm not aware of any place I can view logs of what took place (like you do with the bulk api on yourorg.my.salesforce.com/750).
QueryResult Object ( [queryLocator] => [done] => 1 [records] => Array (  => SObject Object ( [type] => [fields] => [Id] => SFIDHERE ) ) [size] => 1 )
Sample of the query run that produces the above. (line breaks added for less scroll)
$results = $mySforceConnection->query( "SELECT Id, Name, Stage__c, Subtotal__c FROM Custom_Object__c WHERE AccountId = '$Id'" );