The 5v pin on the mega is tied to the power to the chip, so you definitly are getting something there. Measure voltage between the 5v pin and ground.
What are you connecting? How much current is it trying to draw? Could the thing you're connecting be shorted, or trying to draw more than USB can supply?
Actually, if you had something that was sucking down a lot of current when it shut off while running from 8v barrel jack, that would explain what you originally saw, with it working for a while and then turning off - you were putting a heavy load on it, and since the regulator is dropping 3v at heat, it overheated - typically they either foldback the output or turn it off entirely until it cools in that case, rather than the part failing)