I've finally had another chance to look at this. Output of usb reset, usb reset, usb tree, usb info below:
$this->bbcode_second_pass_code('', '
Marvell>> usb reset
(Re)start USB...
USB: Register 10011 NbrPorts 1
USB EHCI 1.00
scanning bus for devices... 3 USB Device(s) found
scanning bus for storage devices... 0 Storage Device(s) found
Marvell>> usb reset
(Re)start USB...
USB: Register 10011 NbrPorts 1
USB EHCI 1.00
scanning bus for devices... 3 USB Device(s) found
scanning bus for storage devices... 0 Storage Device(s) found
Marvell>> usb tree
Device Tree:
1 Hub (480 Mb/s, 0mA)
| u-boot EHCI Host Controller
|
+-2 Hub (480 Mb/s, 100mA)
| USB2.0 Hub
|
+-0 See Interface (480 Mb/s, 0mA)
Marvell>> usb info
1: Hub, USB Revision 2.0
- u-boot EHCI Host Controller
- Class: Hub
- PacketSize: 64 Configurations: 1
- Vendor: 0x0000 Product 0x0000 Version 1.0
Configuration: 1
- Interfaces: 1 Self Powered 0mA
Interface: 0
- Alternate Setting 0, Endpoints: 1
- Class Hub
- Endpoint 1 In Interrupt MaxPacket 8 Interval 255ms
2: Hub, USB Revision 2.0
- USB2.0 Hub
- Class: Hub
- PacketSize: 64 Configurations: 1
- Vendor: 0x05e3 Product 0x0608 Version 9.1
Configuration: 1
- Interfaces: 1 Self Powered Remote Wakeup 100mA
Interface: 0
- Alternate Setting 0, Endpoints: 1
- Class Hub
- Endpoint 1 In Interrupt MaxPacket 1 Interval 12ms
Configuration: 0
- Interfaces: 0 Bus Powered 0mA
')
Any suggestions on what to try next?
Thank you!

EDIT: Incase there is value in this information, here is the UBoot log from a cold boot, which boots into ALARM:
$this->bbcode_second_pass_code('', '
U-Boot 2010.09 (Oct 23 2010 - 11:51:16)
Marvell-PinkPogo by Jeff Doozan
Hit any key to stop autoboot: 0
(Re)start USB...
USB: Register 10011 NbrPorts 1
USB EHCI 1.00
scanning bus for devices... 3 USB Device(s) found
scanning bus for storage devices... 1 Storage Device(s) found
Loading file "/rescueme" from usb device 0:1 (usbda1)
** File not found /rescueme
reading /rescueme.txt
** Unable to read "/rescueme.txt" from usb 0:1 **
Creating 1 MTD partitions on "nand0":
0x000002500000-0x000008000000 : "mtd=3"
UBI: attaching mtd1 to ubi0
UBI: physical eraseblock size: 131072 bytes (128 KiB)
UBI: logical eraseblock size: 129024 bytes
UBI: smallest flash I/O unit: 2048
UBI: sub-page size: 512
UBI: VID header offset: 512 (aligned 512)
UBI: data offset: 2048
UBI: attached mtd1 to ubi0
UBI: MTD device name: "mtd=3"
UBI: MTD device size: 91 MiB
UBI: number of good PEBs: 727
UBI: number of bad PEBs: 1
UBI: max. allowed volumes: 128
UBI: wear-leveling threshold: 4096
UBI: number of internal volumes: 1
UBI: number of user volumes: 0
UBI: available PEBs: 716
UBI: total number of reserved PEBs: 11
UBI: number of PEBs reserved for bad PEB handling: 7
UBI: max/mean erase counter: 1/1
UBIFS error (pid 0): ubifs_get_sb: cannot open "ubi:rootfs", error -19
Error reading superblock on volume 'ubi:rootfs'!
Loading file "/boot/uImage" from usb device 0:1 (usbda1)
1 bytes read
Found bootable drive on usb 0:1
Loading file "/boot/uImage" from usb device 0:1 (usbda1)
2861420 bytes read
Loading file "/boot/uInitrd" from usb device 0:1 (usbda1)
** File not found /boot/uInitrd
## Booting kernel from Legacy Image at 00800000 ...
Image Name: Linux-3.1.10-8-ARCH
Image Type: ARM Linux Kernel Image (uncompressed)
Data Size: 2861356 Bytes = 2.7 MiB
Load Address: 00008000
Entry Point: 00008000
Verifying Checksum ... OK
Loading Kernel Image ... OK
OK
Starting kernel ...
')
And, for completeness, here is the output of usb reset, usb tree, usb info, boot from a cold boot, which
does not boot into ALARM (it would suggest that interrupting the boot process and issuing the usb commands before boot has caused the HDD to disappear?):
$this->bbcode_second_pass_code('', '
Marvell>> usb reset
(Re)start USB...
USB: Register 10011 NbrPorts 1
USB EHCI 1.00
scanning bus for devices... 3 USB Device(s) found
scanning bus for storage devices... 1 Storage Device(s) found
Marvell>> usb tree
Device Tree:
1 Hub (480 Mb/s, 0mA)
| u-boot EHCI Host Controller
|
+-2 Hub (480 Mb/s, 100mA)
| USB2.0 Hub
|
+-3 Mass Storage (480 Mb/s, 2mA)
Super Top USB 2.0 SATA BRIDGE M6116A016V20
Marvell>> usb info
1: Hub, USB Revision 2.0
- u-boot EHCI Host Controller
- Class: Hub
- PacketSize: 64 Configurations: 1
- Vendor: 0x0000 Product 0x0000 Version 1.0
Configuration: 1
- Interfaces: 1 Self Powered 0mA
Interface: 0
- Alternate Setting 0, Endpoints: 1
- Class Hub
- Endpoint 1 In Interrupt MaxPacket 8 Interval 255ms
2: Hub, USB Revision 2.0
- USB2.0 Hub
- Class: Hub
- PacketSize: 64 Configurations: 1
- Vendor: 0x05e3 Product 0x0608 Version 9.1
Configuration: 1
- Interfaces: 1 Self Powered Remote Wakeup 100mA
Interface: 0
- Alternate Setting 0, Endpoints: 1
- Class Hub
- Endpoint 1 In Interrupt MaxPacket 1 Interval 12ms
3: Mass Storage, USB Revision 2.0
- Super Top USB 2.0 SATA BRIDGE M6116A016V20
- Class: (from Interface) Mass Storage
- PacketSize: 64 Configurations: 1
- Vendor: 0x14cd Product 0x6116 Version 2.0
Configuration: 1
- Interfaces: 1 Self Powered 2mA
Interface: 0
- Alternate Setting 0, Endpoints: 2
- Class Mass Storage, Transp. SCSI, Bulk only
- Endpoint 1 In Bulk MaxPacket 512
- Endpoint 2 Out Bulk MaxPacket 512
Marvell>> boot
(Re)start USB...
USB: Register 10011 NbrPorts 1
USB EHCI 1.00
scanning bus for devices... 3 USB Device(s) found
scanning bus for storage devices... 0 Storage Device(s) found
** Block device usb 0 not supported
** Invalid boot device **
Creating 1 MTD partitions on "nand0":
0x000002500000-0x000008000000 : "mtd=3"
UBI: attaching mtd1 to ubi0
UBI: physical eraseblock size: 131072 bytes (128 KiB)
UBI: logical eraseblock size: 129024 bytes
UBI: smallest flash I/O unit: 2048
UBI: sub-page size: 512
UBI: VID header offset: 512 (aligned 512)
UBI: data offset: 2048
UBI: attached mtd1 to ubi0
UBI: MTD device name: "mtd=3"
UBI: MTD device size: 91 MiB
UBI: number of good PEBs: 727
UBI: number of bad PEBs: 1
UBI: max. allowed volumes: 128
UBI: wear-leveling threshold: 4096
UBI: number of internal volumes: 1
UBI: number of user volumes: 0
UBI: available PEBs: 716
UBI: total number of reserved PEBs: 11
UBI: number of PEBs reserved for bad PEB handling: 7
UBI: max/mean erase counter: 1/1
UBIFS error (pid 0): ubifs_get_sb: cannot open "ubi:rootfs", error -19
Error reading superblock on volume 'ubi:rootfs'!
** Block device usb 0 not supported
** Block device usb 1 not supported
** Block device usb 2 not supported
** Block device usb 3 not supported
** Block device usb 0 not supported
** Block device usb 0 not supported
Wrong Image Format for bootm command
ERROR: can't get kernel image!
stopping USB..
### JFFS2 loading 'uboot-original-mtd0.kwb' to 0x800000
Scanning JFFS2 FS: ....... read_nand_cached: error reading nand off 0x13b2a00 s
ize 8192 bytes
. done.
read_nand_cached: error reading nand off 0x13b1600 size 8192 bytes
off = 0x13b128c magic 0x1985 type 0xe002 node.totlen = 2431
### JFFS2 load complete: 524288 bytes loaded to 0x800000
## Starting application at 0x00800200 ...
')