Are you using a Plugin for this? Google Analytics made some modifications to the way they spit out stats awhile back. I know this is affected the Joe Tan plugin worked at: http://tantannoodles.com/toolkit/wordpress-reports/ Perhaps whatever you’re using requires a similar upgrade?
Yes, the ID is in there, and G/A works just fine in general for my site. It’s only the Site Overlay tool that does not work. I actually checked Site Overlay on some of my other wordpress blogs with the date-style of permalink configuration and it doesn’t seem to be working there either. The rest of G/A seems to work just fine.
Has anyone gotten GA’s site overlay to work correctly with their custom-permalinks installation of wordpress?
Yes. On a domain I have 3 separate installation of WP: two in their own subfolders and one in/on a subdomain. All of them are using nice permalinks.
Everything in GA works fine if I enter those 3 URLs as separate “sites” for GA to watch.