I have a similar problem.
One my main domain
7exclusive.com I'm tracking hits and clicks without any problem.
My other site
analgapeteens.com is located on the same server in a submap 'analgapeteens'.
The tracking code is included on my analgapeteens template (when I check the source of the generated index page, I can see that the script is generated).
Now for the problem: Clicks are registered without any problem in Tradepulse of analgapeteens.com, but it doesn't count any incoming hits.
Best Regards,
7exclusive