Thanks for the quick response. I checked the log and didn't see any fatal error. No long running query on in SQL. The DB is quite small 125MB.
The overlay issue appears right after you hit save with a custom field (list) in the search. I can reload the page and it goes back to normal. Existing saved searches are all working fine.
If I edit the problematic custom search and remove the custom field (list), hit save, then that particular search will work and display the count next to it. No issue with overlay. Creating any new search or editing existing one and adding the custom list field will break the saved search and create the overlay.