This is unfortunate. I don’t use this plugin, but it sounds like there may be a simple fix if someone can identify the precise problem(s).
On a quick scan, at least one problem area may be in modules/taxonomy/class.php at line 305. Before this some logic should be added to check for the occurrence of ” AS tr” in the initial $pieces[‘join’] value and if there is we should append " LEFT JOIN tr ON (tr.term_taxonomy_id..."
instead of re-specifying $wpdb->term_relationships AS tr
again.
There may be other occurrences of similar issues elsewhere, but I’m pretty sure this is the direction of a solution.