I just had this problem and this worked for me.
Hope this thread helps somebody.

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 presto - 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.

Like I said, hope this helps somebody.