As well as measuring the input voltage to the Mega, put your finger on the voltage regulator. If it is too hot to keep your finger on for a few seconds, then it is very likely being overloaded - in which case, check what else you are powering from the 5V rail. If it is cool and being fed with 12V but producing only 3.8V output, then it is faulty or there is a bad connection somewhere.
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