I rolled back from 3.2.1 -> to 3.06 and observed that only up to 3.06 version of WP will work with this plugin. Anything beyond will cause page 404. I think the problem lays inside cononical.php and something else.
The plugin won't able to point to the custom link field with WP > 3.06.
Did anyone successfully enabled this plugin beyond 3.06?