To get the plugin to work with permalinks in WP3.1, you need to update the redirect_canonical() function in wp-includes/canonical.php. On line 167 wrap the following code:
$tax_url = parse_url($tax_url);
if ( ! empty($tax_url['query']) ) { // Custom taxonomies may only be accessable via ?taxonomy=..&term=..
parse_str($tax_url['query'], $query_vars);
$redirect['query'] = add_query_arg($query_vars, $redirect['query']);
} else { // Taxonomy is accessable via a "pretty-URL"
$redirect['path'] = $tax_url['path'];
}
in an if (is_tax()) block:
if (is_tax()) {
$tax_url = parse_url($tax_url);
if ( ! empty($tax_url['query']) ) { // Custom taxonomies may only be accessable via ?taxonomy=..&term=..
parse_str($tax_url['query'], $query_vars);
$redirect['query'] = add_query_arg($query_vars, $redirect['query']);
} else { // Taxonomy is accessable via a "pretty-URL"
$redirect['path'] = $tax_url['path'];
}
}