Have you checked your scheduled tasks to see anything that might be running around those times?
Also, keep in mind vbulletin works by itself, however, hacks themselves make appear to work fine but at times may conflict with one another - you may have to try disabling them one at a time - around 4AM if that is when specifically that it stops working. I had a similar issue on one of my boards and it was a hack that was installed that conflicted with another.
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