SMPS regulator blows up, could it be a layout issue?
All the example circuits in the LT3680 datasheet show at least a 4.7uF capacitor directly between Vin and Ground. Your circuit appears to have nothing. 

Since your 'protection' diode prevents current from flowing back into the supply, there is nothing to soak up voltage spikes on Vin except for the IC itself. Combine that with the extra inductance of long thin traces, and... boom!