although only remotely connected, i have problems shutting down my medion laptop when a usb mouse is connected?!? looks like they havent quite got the hang of usb devices hehe.
My only viable suggestion is to enable legacy usb or usb through dos in your bios, that way the drive will be properly recognised in boot up.
Im sure harddrives dont like being switched on without a data connection anyway, but im not so sure on these external devices. Perhaps you could mod the power connection so that it powers up when your pc does? :P