Has anybody else noticed that the first time you add a custom field to the logFile section via the UI, it adds it to the Default Web Site, not the site you're currently administering?
For instance, try adding the equivalent of this to a non-default site. The first time through, it seems to add it to site one. Then when I go back and delete it from site one, I can re-add it the intended site.
<logFile><customFields><clear /><add logFieldName="c-port" sourceName="REMOTE_PORT" sourceType="ServerVariable" /></customFields></logFile>