The Alureon virus and some older variants of Sirefef will place a cloaked, boot partition at the end of the drive. These usually don't show up in the Disk management, but using a boot partition manager, like G Parted will reveal them. The hidden partition is generally 1 - 3 MB in size, although these can be as big as 10MB.
The recommended action for most boot viruses nowadays is to also wipe the drive before reinstalling to eliminate any such hidden partitions.