Sorry for the late reply, it seems I am not getting email notification from the forum for some reason.
You need to look at filters on the site in the custom theme, search code for add_filter or add_action calls. I would start by looking for filters on the hook pre_get_posts an you can search for that as well. These are usually the cause of this problem. At the top of these filters make sure that the code is testing to see if the query is the main query before it alters the query.
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