Hard to say. Hopefully some of the more hardware oriented people will have additional ideas.
Sounds like the Voltage Regulator is probably getting hot. When I have had situations like this it was usually because there was a short somewhere. Or it could be because you are feeding it too high of a voltage and/or devices connected to the board are using too much current.
What I would do first, is to check for obvious shorts. I often use OHM meter and check all of the IOs to ground to see if any shorts. Also check +3.3 to gnd, VIN to gnd, Vin to +3.3 ... If you detect any shorts and resolve them, you might be lucky and the board will work again... Also I would do a visual check of the board looking for signs of something fried, like pot mark in an IC or...
Sometimes I have been lucky and once a short was resolved, everything was fine. A few times I replaced the board. BUT, before using a replacement make sure the condition that killed the first one is not still present.
Good luck.