I recently noticed that on one of my MOSS 2007 server farms any time I tried to view Audit Log reports I would get the error:

The specified Web does not contain a reporting metadata list.

My theory is it is happening on sites I've created using a custom template, but I haven't fully tested that. Either way, the solution is the run the below command on the server in question:

stsadm -o activatefeature -name Reporting -url http://yourserver/sitecollection/ -force

I was getting the error even though auditing was already enabled, so luckily all the audit logs were being stored in SQL even though I could not view them via the reports. Once I ran the above command all the past logs were available.

Of course you could script this to run through all the site collections in your web app(s) to ensure reporting will work going forward.