There is something a bit weird I noticed lately: When the message 'Question with new activity' pops up at the top of the questions list and I click the 'Questions' button instead of the message itself, the new question mysteriously vanishes for a few minutes or so, no matter how often I click 'Questions' again. Basically it looks like the polling time for the bar is much shorter than that for the 'Question' button. Did anybody notice this?
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This is by design.
The Questions page is heavily cached, so it can take a couple of minutes for new questions to appear.
Since pushing new questions via Web Sockets is a lot less expensive, there's no caching (or less) and they appear much faster this way.
The obvious solution is: Don't do that.
Real-time updates have been designed specifically to prevent this delay and reduce the load on the servers.