On the DUE there is a switch mode regulator from 12v to 5v. If board is powered from USB first then no problems if 12v applied. If powered first from 12v, and supply loading is low, ... no shields or other things loading the 3.3v, then OFTEN, there will be 600mV ripple, at 10Khz, on 5v supply and 500mV ripple on 3.3v supply. I traced it back to light loading on switch mode regulator. A permanent fix is to put a 4.7uF electrolytic across the 3.3v supply. This forces the switch mode circuit to see a high load at power up and it works correctly. Both the original DUE and the Chinese knockoff have the same problem.
2.
AT power up, comms processor waking up before/after main cpu can cause a problem requiring reset button to be used. If a standalone system is 1000KM away, this is really hard to fix!! Using a power up reset circuit, that holds the reset line low for at least 75mS, so that the power supplies are stable, solves the problem. This needs either a standard CPU reset chip, or a transistor, 2 resistors, a capacitor and a diode(for instant recovery with a brownout.
5v.... + 4.7uF -<- 22K -->- base of npn BC847 transistor, 22K to 0v, cathode of diode bas16, diode anode to 0v, transistor emitter to 0v, and transistor collector to reset line. This holds in reset for 150mS.
