Pretty sure it won't just be the mass storage device contents that are causing the problems. More like the USB driver supplied by the stick when plugged in does the infecting. And you don't see that when you download the stick's contents.
And if you don't exactly hit the conditions the malware is supposed to expose itself, you have no way to read out the EEPROM inside the flash controller. The data chips maybe, but the controller chip of a USB stick is an entirely different thing.
And we all know that USB sticks (or, rather their flash chips) can be reprogrammed at will. USBest, I'm looking at you. (See also flashboot.ru, the stuff you can do with these tools is amazing.)
1) Hides a bootloader on the devive that runs at reboot (assuming the BIOS allows it).
2) Pretends to be some kind of device (that most OS's have stock drivers for) that allows it to access main memory. Maybe it pretends to be a USB to firewire bridge (or something similar that gives it DMA).
Assuming a government is the adversary (and we ALL know that the NSA sits on a very comprehensive list of exploits!), then this part is actually the easiest.