Also having same issue...
I am also having the same issue. I believe it began when I created a new site (web20) under client2. I looked at stats directory and noticed it was empty after getting a 403 forbidden message when accessing it from new site. I noticed that the stats directory on web20 was owned by root root, so I changed it back to web20 client2 and waited a few days, but nothing has appeared yet.
I then checked my other sites and it seems they stopped logging the same day I created that new site (web20). Directory is still empty and stats are no longer being created on my other sites.
Any ideas or suggestions?