Hi!
I have a module in the position "feature-a". I have set this to be present on the frontpage only.
The module is only present on the first page, but this is not removed:
<div class="rt-feature">
<div class="rt-container">
<div class="clear"></div>
</div>
</div>
Looking in the index.php of the template I find this:
<?php /** Begin Feature **/ if ($gantry->countModules('feature')) : ?>
<div id="rt-feature">
<div class="rt-container">
<div class="clear"></div>
</div>
</div>
<?php /** End Feature **/ endif; ?>
This part: $gantry->countModules('feature') seems to always return "1" or higher. If I have two modules in the feature section it returns "2". If I have 1 it returns 1. If I have 0 it returns "1".
Supposed to be this way? 
EDIT:
I'm using J1.6 with the default Gantry template