Help please

Hi. Need help please...
Why would my mega work fine when powered from usb. But it burns regulator when connecting to a 12vdc supply through the jack?

Because you're wasting seven volts at whatever current you are drawing.

Nope. Its rated for 12v

Despite the rating a lot of us run around 8-10 volts so the regulator has less voltage to dissipate as wasted heat.

Some cheaper or older PSU's "spike" when turned on which is hard to see on a multimeter but easy with a scope.

Nope. Its rated for 12v

I think you misunderstand. The voltage regulator brings the input voltage down from 12V to 5V. The board draws roughly (thumbsuck, never measured it) 50 mA. So the regulator needs to dissipate 350 mW (7 x 50) and will happily do so.

Once you start powering other stuff from the 5V pin, you somewhere reach the limit if what can be dissipated and the regulator will overheat.