Ok, this is very important!

The solution was adding this to the query:

$nodeQuery->addMetaData('account', user_load(1));

As I mentioned I was running the code in the context of a Services module resource request. Looks like that I am prevented from filtering on a particular field, however not prevented from getting everything if I don't specify filter just load all and use node_load.

Its a real shame, no comment.

Ok, this is very important!

The solution was adding this to the query:

 $nodeQuery->addMetaData('account', user_load(1));

As I mentioned I was running the code in the context of a Services module resource request. Looks like that I am prevented from filtering on a particular field, however not prevented from getting everything if I don't specify filter just load all and use node_load.