If your experiencing trouble with a domain on your cpanel server, where the domain's webalizer has failed to run for, say, a year (or whatever), you can attempt to manually fire webalizer for that particular account.

Just log into the box, switch user (su -) to root, then type /scripts/runweblogs (without the quotes) at the command prompt.
Then type the account username when prompted, hit enter, and the domain should now have current stats.
Go and check (or read the message returned to you).

If that fails to produce stats, then try running the command /scripts/fixwebalizer
You'll loose everything (in my case, it actually lost everything - except for most of the last day of the previous month, also, the current month was generated in it's entirety). Though what it lost in my case was data from a year and a half ago, so it wasn't so sad to watch it go.