I found the answer here. They were having the exact same problem:
Using tax_query reverses my post_type argument in a custom WP_Query
It is a problem with the Easy Content Types plugin. Pippin, the author of this plugin wrote the following: The problem is caused by a function in the plugin that helps to resolve taxonomy archive 404s. It has a couple of issues, and because of them, there is a setting to disable the function. Go to Content Types > Settings and check “Disable Taxonomy Archive Fix”. – Pippin May 11 ’12 at 0:03
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