Upgraded to 2.0.9 from 2.0.7. I'm using this code just inside the loop to "hide" one category:
<?php if (in_category('7')) continue; ?>
In 2.0.7, with that code in place, and with 5 posts selected in the admin/options/reading section, 5 posts showed on the index page. In 2.0.9, with that code in place, and having run upgrade.php and updated the 5 posts selection in admin/options/reading, there's only one post showing on the index page.
I did recheck The_Loop to be sure nothing had changed with that usage. It seems to be correct.... I also checked the database to be sure the options row updated for that selection, which it did.
Any help appreciated!