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There was a short period of time where we sent out a zip containing a messed up sitemap.php that I forgot to set back after some testing. It was actually fixed in one of the updates. Open up that file, and inside you'll see
$i = $i + 40;
change it to
$i = $i + 40000;
As for why you only have a few thousand indexed - the formatting is all correct, it just takes a couple weeks or more for google to actually index it all. If there is any error in the sitemap xml webmaster tools throws an error.
That being said, it's usually easier to catch us on our support ticket system...
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