Hmm... I'm not sure how a hidden partition on a flash drive failed to get any Windows users' attention. Windows sees USB flash drives as "superfloppies" (as opposed to hard drives), and therefore will only detect the first partition on the device (The other partitions won't even show up in the Disk Manager (diskmgmt.msc)). If it mounts infected partition, the partition that actually has useful data would be ignored, which would surely raise some eyebrows. If the non-rogue partition is mounted, there's no way the infected partition could be a threat. Perhaps the infection overrides this behavior, by forcing Windows to unmount the first partition and mount the second?