Not sure if this helps but we've just had a similar problem.
Stats appeared to run but data was not being inserted into our stats_user_daily table.
We had a problem with the data that was being compiled in the temporary tables (lib/statslib.php).
Turned out one of our activities was entering a userid as -1. The stats_user tables datatypes are bigints and it could be our setup (mysql bug?) but it prevented our stats from compiling.
We changed the userid field in the stats_user_daily/weekly/monthly tables to a different datatype (we've gone with varchar(25) until we locate the offending activity and remove it) and our stats are processing happily now.
Hope this helps someone!