(note: I've seen the related question on area51 vs stackexchange.com/sites traffic reporting. This is a slightly different discrepancy).
For cstheory.stackexchange.com, the site stats listed on the home page currently list 3129 visitors/day (and this number has been relatively steady). I occasionally visit stackexchange.com/sites to look at the relative performance of the site, and there saw a listing 1.5k visits/day, which is about half the number listed on our home page. This lower number also matches area51 stats for our site.
I was wondering if the home page formula has not changed over like the s.e/sites formula has ? Because the two used to match.