i connected a TLC7705IP as a power on reset and it fixed the starup problem. i used the 7705 which ihas a voltage threshold of something like 4.6 volts. it is powered by the 3.3 volt supply so its logic levels are 3.3 volt compatible but it has the sense line on the 5 volt supply. i had to use a large timing capacitor of 4.7 mf to hold the reset high for something like .5 seconds. anything much shorter does not work.
i do think that this should not happen with the DUE board. it should properly use the various brownout and startup capabilities of the SAM micro. it is not a big deal to add this chip but the board is supposed to be a working system and have these details worked out. i hope future revisions of the board do not have this problem. otherwise i am very pleased with the DUE.