Nope, It not under the preferences box anymore. Just the 3 links. I dont even have a count of how many messages are in my inbox.
Can you right click in the page (under the My Messages section) and select "View Source". This should open up Notepad with the actual HTML source code for the page itself. Hold down your CTRL key and press the letter f (this should open up a find box). Type in "Prune Messages" without the quotes. After it highlights, scroll down and see if you have something similar to the following:
<a href="http://www.ohioreef.com/index.php?action=pm;sa=manlabels">Manage Labels</a><br />
<a href="http://www.ohioreef.com/index.php?action=pm;sa=prune">Prune Messages</a><br />
<br /><br />
<div align="center">
<b>Capacity</b>
<div align="left" style="border: 1px solid black; height: 7px; width: 100px;">
<div style="border: 0; background-color: #468008; height: 7px; width: 23px;"></div>
</div>
<span>23 messages, 23% full.</span>
</div>
In my case (shown above), I have 23 messages. If your's lists something, it narrows it down to a display issue (possibly a browser issue). If it doesn't list anything, might be something else entirely.
Jerry