Yes, for us who use TP index.php != index.php?action=forum but for a normal SMF user those are the same.
And exactly that's the problem.
From the index.template.php
// Please don't index these Mr Robot.
<meta name="robots" content="noindex" />';
Since for the forum (plain smf) both are the same site, the meta tag will be shown on index.php?action=forum but not for index.php. Or atleast those are my conclusions after observing this behaviour.
As for the robot stuff, it's a simple tag in order to prevent crawlers from indexing that site. SMF does this in order to prevent the same site being indexed multiple times (I checked on their forums).
A quick fix would be excluding index.php?action=forum from the "noindex" list, wherever this is located. But I think TP should do this by default on installation.
Right now, the forum index page won't be indexed/crawled by bots with this configuration.
Edit: I've checked the source code for tinyportal.net, the same thing happens, the main forum view has the noindex tag active.