From the troubleshooting i have done, i believe the problem is on the back-end. Meaning, on the server where the stats are being hosted. Meaning, wordpress.com.
I have two domains, otherwonders.com and sneakykitty.com. If i create test blogs on otherwonders.com and on subdomains of otherwonders.com, the stats all show up just as they ought to – separate stats for each subdomain, which are also separate from the primary domain.
But if i set up test blogs on subdomains of sneakykitty.com, they all get merged with the stats for sneakykitty.com. The only exception to this is a subdomain where i first installed the stats plugin; the sneakykitty.com blog had the plug-in installed later.
I’ve emailed their support with all of the information i had, and received no response. It’s possible that they’re just backlogged, but it’s been a week or two. I am not sure how to resolve the issue, or if it is even possible to do so. I’m looking into other statistic management systems, but unfortunately, nothing collects the same type of data (and amount of data) that i’m trying to get.