Just thought of sharing this MSDN forum-thread with my blog followers since I have received this question more than once. Usage Analysis is really a common source of confusion among SharePoint administrators.

Q :

I have 3 Web Applications, webapp1, webapp2 and I recently added webapp3. each web application hosts about 5 site collections.
I have enabled usage analysis processing  on the farm level but it’s only capturing information for web app1 and web app2. And it’s not capturing any information for any site collection for web app3.

A :

Usage reporting from within MOSS runs on a daily schedule that is user configurable from the central administration, you must wait at least one day for any meaningful reporting to be available for new web application. By the way you should activate the reporting feature on all the site collections in the web application.

Q :

I have already activated the reporting feature on all the site collections and about 48 hours elapsed to collect the usage statistics.

A :

Run the following commands from the command prompt, wait for 24 hours and it should work.

stsadm -o setproperty -pn job-usage-analysis -pv no

stsadm -o setproperty -pn job-usage-analysis -pv yes

This sequence disables, then re-enables the job-usage-analysis job within SharePoint. It’s important to execute this sequence after adding new web applications.
Let me know after 24 hours.

Q :

Now the new web application usage info is captured.

A :

Note that when you add a new Web application to MOSS, usage analysis is not automatically reconfigured. In order to make usage analysis processing available for the new Web application, you must disable, then re-enable via central administration or through STSADM as I showed you.