Index: primary_term/primary_term.module
===================================================================
--- primary_term/primary_term.module	(revision 540)
+++ primary_term/primary_term.module	(working copy)
@@ -37,7 +37,9 @@
     case 'insert':
     case 'update':
       db_query('DELETE FROM {primary_term} WHERE vid = %d', $node->vid); // only one term per node revision
-      $primaryterm = _primary_term_get_tid($node);
+      //in this cas we only want primary term from the node form
+      //because _primary_term_get_tid return previous value when 'none' is selected
+      $primaryterm = $node->primaryterm;
       if (! empty($primaryterm)) {
         db_query('INSERT INTO {primary_term} (vid, tid) VALUES (%d, %d)', $node->vid, $primaryterm);