I have my webalizer stats now.
I installed ISPConfig a few days ago onto Ubuntu 9.10 64 bit and getting on fine with it after a few operator errors.
I've had the same problem with getting webalizer stats being produced just as previous writers mentioned.
I did notice in the ISPConfig cron.log that GEOip.dat could not be found at /usr/share/geoip so the ISPConfig cron.daily did not run properly. Seems this was not installed so I installed it with apt-get install geoip-database.
I ran the cron.daily script and my webalizer files are in the /stats folder now and I can access them as I should.
Sorry this is a few months late but I read through the forums and didn't see this mentioned as a possible solution.