When querying for logs, regardless on what machine you're on, query goes to the log servers.
When running views and reports, queries are running against the SmartEvent server.
In order to make sure logs really got to the SmartEvent Server, open a view, and drill down by double clicking one of the widgets.
You should see the logs (if you get a view, drill down further), but you should notice also a "Session Only" tag.
This tells the SmartLog to look for logs on the SmartEvent machine.
Now you can clear the "drill down" filter, keeping the "Session Only" tag, and run custom query to see what really are the logs that indexed in SmartEvent.