Well I first noticed this problem after upgrading to WordPress 2.5 (probably upgrading WP-Stats at the same time), and after finding this thread I went through and re-saved the majority of my posts as a temporary fix.
I've just upgraded to WordPress 2.6 and WordPress.com Stats 1.3.2, and it's happened all over again!
Has anyone had any luck figuring this one out? Re-saving every single post after every upgrade is extremely tedious when there are lots of them. If there's a simple query I can run on the DB I'd rather do that instead, or just have the bug fixed except it's not clear to me who I should be reporting it to. Alternatively if anyone knows of a plugin that will automatically do the equivalent of hitting the Save button for 200+ posts, perhaps it'd be a useful workaround.
I wonder if it's something to do with using a custom permalink structure.