The more recent 2.6 kernels don't just issue a "power down" to all (IDE?) discs when halting the machine but also when rebooting it. This is suboptimal since it reduces the discs lifetime (though this is probably negligible compared to the expected start-stop counts of modern drives) and increases the reboot duration (the BIOS has to spin the disks up again which can take several seconds for each drive) A corresponding bugzilla (https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=122966) entry on redhat also talks of BIOS which timeout while the drives spin up.
This seems to have been fixed in 2.6.7rc1, see http://linux.bkbits.net:8080/linux-2.5/diffs/drivers/ide/ide-disk.c@1.80?nav=index.html|src/|src/drivers|src/drivers/ide|hist/drivers/ide/ide-disk.c