I'm using version 1.3.1 alpha 2. The primary difference (visually) is that the widget already displays the first term in the list of terms in each taxonomy drop-down. On alpha 1 this area was blank.
Secondly, when performing a query (any query), I am getting the following:
Fatal error: Call to undefined function debug_lq() in /home/wwwappl/public_html/wp-content/plugins/query-multiple-taxonomies/core.php on line 135
The site is visible at http://durban.directrouter.com/~wwwappl/