How to tell Custom Breadcrumbs which vocabulary to use?
I had the same problem on my site. I managed to fix it the hard way.

Edit custom_breadcrumbs_taxonomy/custom_breadcrumbs_taxonomy.inc

Add these lines after line 20:

$query-&gt;condition("v.vid", 2); // 2 is the id of vocab You want to use
$query-&gt;orderBy('v.weight');
$query-&gt;orderBy('t.weight');
$query-&gt;orderBy('t.name');


So You have:

...
$t_alias = $query-&gt;join('taxonomy_term_data', 't', 'r.tid = t.tid');
$v_alias = $query-&gt;join('taxonomy_vocabulary', 'v', 't.vid = v.vid');
$query-&gt;fields( $t_alias );
$query-&gt;condition("r.nid", $node-&gt;nid);
$query-&gt;condition("v.vid", 2);
$query-&gt;orderBy('v.weight');
$query-&gt;orderBy('t.weight');
$query-&gt;orderBy('t.name');
$result = $query-&gt;execute();
$terms[$node-&gt;vid][$key] = array();
...