Hi Travis,
me too I've problems with Arduino Due Host example.
First all, I'm not able to find the HOST_EXAMPLE21 of Palliser, but no problem, I compiled the Atmel ASF example and installed it into my arduino but me too I've not soft event.
Atmel said to me to format my Pen drive as FAT32 and try again, also with other Pen drive but for now anything of positive happens :).
Good luck and please tell me if you are able to run the USB Soft software.
best regards at all
Davide