jdMorgan - 4:25 pm on Apr 3, 2010 (gmt 0)
Webalizer uses the raw server access logs as input, and therefore can't log anything that didn't happen.
Have look at the scope of your "Deny from" directives -- Are they enclosed in any containers such as <Files>, <FilesMatch>, or <Limit>? If so, a common problem is that those containers are "wrong."
In .htaccess, you may use only one "Order" directive within the same scope. Otherwise, only the last one found will apply. Also, it is a common problem that webmasters use the wrong "Order" -- I suggest using "Order Deny,Allow" and adjusting the Allow and Deny directives to suit. If "Allow from all" appears in your code, it's likely that you have this problem.
The root problem that causes so many sites to have errors is that webmasters copy bad code from forums, use it on their sites, and then re-post that code in other forums, and the bad code spreads because no-one ever bothers to check that code against the documentation at apache.org and to really understand it before using it.
Even common "control panels" often produce malformed, badly-scoped, and/or inefficient code. Code distributed with many forum, blog, and CMS packages is often sloppy and/or really inefficient as well. Therefore, it's quite fair to say that most sites have bad code on them... in many cases, *very* bad code.