I have 2 category groups (ids 8 & 9) assigned to the same channel (although that doesn’t matter from my testing) and I want to output a separate list of each group in the same template.  So I have:

<select>
{exp:channel:categories channel="support_download" category_group="8" show_empty="no" style="linear"}
<option value="{category_url_title}">{category_name}</option>
{/exp:channel:categories}
</select>

<select>
{exp:channel:categories channel="support_download" category_group="9" show_empty="no" style="linear"}
<option value="{category_url_title}">{category_name}</option>
{/exp:channel:categories}
</select>

I should get one list with c5t, CL910 and F5t and another list with only Windows 7 like below:

<select>
<option value="c5t">c5t</option>
<option value="cl910">CL910</option>
<option value="f5t">F5t</option>
</select>

<select>
<option value="windows-7">Windows 7</option>
</select>

But the second tag is outputting all of the categories combined:

<select>
<option value="c5t">c5t</option>
<option value="cl910">CL910</option>
<option value="f5t">F5t</option>
</select>

<select>
<option value="c5t">c5t</option>
<option value="cl910">CL910</option>
<option value="f5t">F5t</option>
<option value="windows-7">Windows 7</option>
</select>

I dumped the $this->cat_array variable on line 382 of Publisher_channel_categories.php and Publisher is definitely loading the categories combined into one array in the second tag.  I also tried the same tags without publisher enabled and they worked as expected (There was no combining of categories).  I test with the tags exactly as written above with nothing else in the template.