Well, this has been a long and unproductive weekend with major frustration in trying to accomplish what "should" be a simple task in Drupal 6.

I posted a couple of issues over the weekend related to the problem as it evolved from Friday night to Saturday, even ending up on Sunday spending some time in the IRC channel searching for the answer.

The related issues on drupal.org are 497636 and 497530. The issue itself was not easily apparent in my initial work on the Taxonomy Rockstar module. What I'm trying to accomplish at this point is only laying down code for the backend interface, and the API that will allow developers to extend the modules using an easy API to create new layout types and search filters for taxonomy presentation.

The Real Problem

At first the problem seemed to be related to my hook_theme function and somehow it not sending the appropraite $element to the function I created for theme_checkboxes.