There are a couple of possibilities. The first is that you are probably booting off the USB drive, and not the internal hard drive! The OS is then, quite understandably, confused over what it should do. The disk's device nodes are probably altered too. The solution would be simple - get into the machine's BIOS and alter the boot order.
Another possibility is that the machine has scsi disks, and the addition of a usb device bumps the /dev/dan nodes along one. I cannot see that happening, though - if a system prioritized usb disks above scsi ones, well......
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