I have three WP blogs on my domain:
1. http://sneakykitty.com
2. http://babble.sneakykitty.com
3. http://fibro.sneakykitty.com
I have the WordPress.com Stats plugin enabled on all three sites.
All three sites are running WP 2.5.
All three sites are running the same theme - different headers, slightly different CSS, but ultimately they all have the same footer.php. And yes: the footer.php does have the <?php wp_footer(); ?>
Site 2 will always display properly.
Site 1 will display correctly if i turn off stats on Site 3.
Site 3 will display the correct stats if i turn off stats on Site 1.
In the dropdown menu that enables you to quickly switch between sites, it only ever lists 1 & 2.
If Stats are turned on in all three sites, 1 & 3 will show the exact same information and list it as being stats for 1. Basically, it's merging the data for the two sites.
Several months ago, i had the same problem with a different blog on a different subdomain (it was later deleted and replaced by # 3). So this problem is not unique to the fibro.sneakykitty.com domain/blog.
Does anyone have any ideas on how to fix this?