Even though my idea did not work out, I'm pleased it got you onto a track that did work.
On the issue with WP_Query, I don't know if this is the actual problem, but it's something to address anyway. You should not supply your taxonomy as a query argument anymore. This technique was deprecated as of version 3.1. Instead, use the various 'tax_query' arguments to specify your taxonomy. With any luck, this will easily fix your query issue and you will not encounter any more mysteries.