External USB 3.0 harddrive as root misdetects available partitions

Hardware:
Asus N53S
WD Passport 0730 (500gb hybrid drive w/ usb3.0)

Procedure:
1) GRUB boots, drive detected
2) Kernel loads
3) Kernel detects sda1 and sda3 (skipping sda2)

GRUB tab completion:
(hd0,0) ext2
(hd0,1) unknown

fdisk output:
primary partition 1 bootable, ext2
primary partition 2 0x8e (linux lvm)

from kernel init:
ls /dev/|grep sda
sda1
sda3

I've tested this with multiple kernel versions which work with an internally (sata 3gb/s) connected laptop hdd. Reverting to a usb 2.0 port does not solve the problem.

Anyone have any clues as to what's going on here?

I've also tried this in VirtualBox which demonstrates the same behavior when you create a device linked straight to the external harddrive.

*edit*

The init:
#!/bin/busybox
mount -t proc none /proc
mount -t sysfs none /sys
mount /dev/sda2 /mnt/root
umount /proc
umount /sys
exec switch_root /mnt/root /sbin/init

I've tried modifying the above to reference sda3 instead, but then it says "cannot open for read-only access"

I should also note that the filesystems on partition 1 is ext2. That's pretty standard for a boot partition. When reformatting the whole of sda2 to fat, ext2, or reiserfs directly without lvm, all of which have kernel built-in fs support, this remains an issue leading me to suspect the usb3 driver.

Setting up /etc/fstab to use device ID's is not a good idea, because the id can change when you add/remove drives. IE, mounting /dev/sda1 is not a good idea. What I do is to boot into a live/rescue CD/DVD, create a label on each partition, mount the root partition, edit the /etc/fstab to use LABEL=partition-name instead of /dev/sda1, /dev/sda2, etc. Then, adding/removing storage units will not munge your file system mounts. You can also use UUID's instead of labels if you prefer, but myself I like to use labels as that makes it easier to move/replace storage units.

I can appreciate that. Ultimately, that depends on how rigid you want the definition to be. That having been said, the fstab preferences are only relevant once switchroot has been run, which is the problem at present. This precludes either of our preferences. :)