Issues with template->destroy and template->set_custom_template

I have a mod that instantiates a new template object then recursively uses the object to display different blocks, setting a new custom template path (template->set_custom_template) for each block, setting a template file (template->set_filenames), destroys the template, then starts over again. It would look something like this:

$mtemplate = new template();

foreach ($blocks as $row)

{

      $mtemplate->set_custom_template(...);

      $data = call_block_function($row);

      $template->assign_block_vars('sidebar', array(

            'BLOCK_TITLE'        => $data['title'],

            'BLOCK_CONTENT'  => $data['content'])

      );

      $mtemplate->destroy();

}

This worked fine prior to 3.0.6 but as of 3.0.6-RC1, destroying the template leads to template issues: Some blocks turn up blank, some variables are not assigned and things like that. I have to destroy the template because some blocks are called more than ones and use the same template file to display different things based on the block settings. I have not been able to figure out the problem but it almost seems when the template is destroyed, template->set_filenames must be set first (which is inconvenient in some instances) prior to assigning any template variables. I'm I missing something or do I smell a bug?