Hi,
Thanks for the details, very helpful!
Okay, this one turned out to be a very interesting issue, completely unrelated to the plugin. Long story short the query was correctly executing, the filters were also set right, so it took me about an hour to figure it out.
Turns out there is an extremely rare MySQL termination/optimization bug with subqueries when using a query limit 1 (that is used in the custom field queries). I had to make a change in the code to overcome this.
It is a tiny change only, and will be included in the upcoming release in case someone else runs into this super rare issue.