There is no Notifications widget, so I'm not sure what to tell you there.
Have you looked in the database to see how many rows are in the searchcore* tables? If you have all forums set to be indexed, you should have at least as many rows in there as you have rows in your post table. If you don't, then my guess would be that when you rebuilt the search index, it timed out and didn't finish.
If you are in control of your server (can make configuration changes), then I would suggest posting in the server configuration forum on vbulletin.com for help configuring your server.
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