Did you have the USB connected at the same time as the 4.8V? Is it possible that the USB was trying to supply power to the 4.8V supply?
Was the 4.8V connected to the 5-9V in (J9p16) or the 5V USB out (J9p10)? If to J9p10, I would expect smoke because the USB 5V would be trying to drive the 4.8 V power supply which would likely be clamping (shorting) the 5 V to ground to get it back to 4.8V.
OR, even though you had connected both sources previously without incident, it is quite possible that previously you had connected the 4.8 V first and then the USB which would cause the FRDM to run on the 4.8V. But the last time you connected the USB then the 4.8V which would cause the USB to supply the FRDM and perhaps then try to drive the 4.8V PS higher. (Or visa versa.)
If that is not the problem, make sure you know how your 3.3 V supply is being used.
I got smoke from a FRDM-KL25Z once when I connected an external switch incorrectly and, evidently, shorted 3V3 to ground. Believe it or not, after connecting things correctly, the board still worked.
Another time, after an interface board redesign, the device I was building worked for a few minutes, then D2 on the KL25Z board blew up. That is the diode that supplies 3V3. Evidently, the interface board drew too much current, or the 3V3 was unhappy about something else (perhaps those durn switches again). ;-(
Another possibility, might be that you had two USB cables connected from two different devices and they did not have a common ground. That might also allow current to turn to smoke and escape the board forever. ;-)
Obviously, you were drawing too much current somehow. Is it easier to try to solve that problem or move on to a better design?
G'luck.