I didnt check codes for what is wrong. but there is a live example:
http://kremim.com/marka/bioderma/konu/temizleyici-urunler/
This page using 2 tax filter;
* 1 "marka" taxonomy as "bioderma"
* 1 "konu" taxonomy as "temizleyici-urunler"
$wp_query->found_posts result is 29 but plugin shows 15 because system pagination is 15.
http://wordpress.org/extend/plugins/query-multiple-taxonomies/
using 1.6.2 version