Under Drupal 6.1
While in general this works fine, we found that if you had a node in a taxonomy, and deleted it, the counter still showed "(1)" for that taxonomy. The seemingly simple solution was to disable and re-enable "Display number of nodes per terms" and the counters seemed to reset.
Comments
Comment #1
indytechcook commentedPlease try the newest version of Taxonomy menu and open an new issue if this is still a problem.