i don't which voltage you use for triggering the POR chip is that important. all that is important is that you reset the microcontroller after a reasonable delay after power is applied. of course you need a voltage that matches the threshold of the device. they come in a few different thresholds to work with 3.3 5 and maybe other voltages. i use a fairly large capacitor for a long delay just to be sure. it has worked absolutely reliable. i used a dip version but i am sure you can get surface mount if space is a problem and use a tantalum cap if there is no room for an electrolytic for the timing cap. make sure the POR chip never sees sense voltage without its power supply connected. i made a shield with some of those crappy thin pin stackable headers that came with the dev shield and a bad connection to 3.3 volts killed the POR chip. not much of a loss but a waste of time figuring out why it didn't work. since then i found some better square pin stackable headers.
it seems to me that this startup problem is a bug with the DUE. are there any configuration options that might fix this in the microcontroller instead of forcing us to add POR chips?