Ok.
Obrigado a todos que tentaram ajudar.
Parece que isso não tinha muito a ver com o Ubuntu, e era basicamente um bug da BIOS.
Algumas placas-mãe Gigabyte gravam uma cópia de seu BIOS em discos rígidos imediatamente quando os discos são conectados. Então, simplesmente conectando um novo HD na placa-mãe é provável que ele seja gravado, e a HPA será ativada reduzindo o tamanho do disco.
O Ubuntu 10.04 por padrão ignora o HPA (libata.ignore_hpa = 1 parâmetro do kernel) e assim tratou o disco inteiro como se não tivesse HPA ativado, usando todos os setores do disco.
O Ubuntu 14.04 por padrão honra o HPA (parâmetro do kernel libata.ignore_hpa = 0) e assim tratou o disco como se fosse menor do que realmente é.
Os discos foram originalmente particionados do formulário 10.04 para a soma total de setores. Alterar o cabeamento resultou na ativação do HPA em todos os discos do RAID.
Tive muita sorte porque o particionamento original não usou todo o espaço disponível, mas deixou espaço suficiente no final da unidade para os setores que a HPA estava roubando. Não sei porque, talvez estivesse se alinhando ao cilindro anterior ao último.
A solução que concluí, era reparticionar as unidades como se fossem menores do que realmente são, tão grandes quanto são feitas pela HPA. Eu inicio a 14.04 e consertei as partições com o gedit.
O processo foi muito perigoso e poderia potencialmente destruir todos os meus dados.
NÃO REPETIR SE VOCÊ CUIDAR DO CONTEÚDO DOS CONDUTORES.
Depois que eu consertei todas as três unidades, ambos os sistemas operacionais poderiam usar o ataque, então eu realmente instalei o 14.04 no disco rígido. Quando eu iniciei em 10.04 os utilitários de particionamento reclamaram que eu não estava usando todo o disco, mas perguntavam antes de alterar qualquer coisa, então nenhum dano foi feito. Para consertar esse pequeno inconveniente eu adicionei libata.ignore_hpa = 0 aos parâmetros do kernel do meu /etc/default/grub.conf para 10.04 e atualizei o grub.
Apenas para o histórico, aqui está o processo PERIGOSO que usei para converter o esquema de partições do disco para / dev / sda (era o mesmo para todas as unidades):
root@ubuntu:/cdrom/HPA_recovery# gdisk /dev/sda
GPT fdisk (gdisk) version 0.8.8
Warning! Disk size is smaller than the main header indicates! Loading
secondary header from the last sector of the disk! You should use 'v' to
verify disk integrity, and perhaps options on the experts' menu to repair
the disk.
Caution: invalid backup GPT header, but valid main header; regenerating
backup header from main header.
Warning! One or more CRCs don't match. You should repair the disk!
Partition table scan:
MBR: protective
BSD: not present
APM: not present
GPT: damaged
****************************************************************************
Caution: Found protective or hybrid MBR and corrupt GPT. Using GPT, but disk
verification and recovery are STRONGLY recommended.
****************************************************************************
Command (? for help): ?
b back up GPT data to a file
c change a partition's name
d delete a partition
i show detailed information on a partition
l list known partition types
n add a new partition
o create a new empty GUID partition table (GPT)
p print the partition table
q quit without saving changes
r recovery and transformation options (experts only)
s sort partitions
t change a partition's type code
v verify disk
w write table to disk and exit
x extra functionality (experts only)
? print this menu
Command (? for help): r
Recovery/transformation command (? for help): ?
b use backup GPT header (rebuilding main)
c load backup partition table from disk (rebuilding main)
d use main GPT header (rebuilding backup)
e load main partition table from disk (rebuilding backup)
f load MBR and build fresh GPT from it
g convert GPT into MBR and exit
h make hybrid MBR
i show detailed information on a partition
l load partition data from a backup file
m return to main menu
o print protective MBR data
p print the partition table
q quit without saving changes
t transform BSD disklabel partition
v verify disk
w write table to disk and exit
x extra functionality (experts only)
? print this menu
Recovery/transformation command (? for help): d
Recovery/transformation command (? for help): p
Disk /dev/sda: 5860531055 sectors, 2.7 TiB
Logical sector size: 512 bytes
Disk identifier (GUID): 2D50CD70-85F5-46FE-85B3-35A027E3C828
Partition table holds up to 128 entries
First usable sector is 34, last usable sector is 5860533134
Partitions will be aligned on 8-sector boundaries
Total free space is 5070 sectors (2.5 MiB)
Number Start (sector) End (sector) Size Code Name
1 34 73658024 35.1 GiB EF00
2 73722285 5860528064 2.7 TiB FD00
3 73658025 73722284 31.4 MiB EF02
Recovery/transformation command (? for help): x
Expert command (? for help): ?
a set attributes
c change partition GUID
d display the sector alignment value
e relocate backup data structures to the end of the disk
g change disk GUID
h recompute CHS values in protective/hybrid MBR
i show detailed information on a partition
l set the sector alignment value
m return to main menu
n create a new protective MBR
o print protective MBR data
p print the partition table
q quit without saving changes
r recovery and transformation options (experts only)
s resize partition table
t transpose two partition table entries
u Replicate partition table on new device
v verify disk
w write table to disk and exit
z zap (destroy) GPT data structures and exit
? print this menu
Expert command (? for help): e
Relocating backup data structures to the end of the disk
Expert command (? for help): ?
a set attributes
c change partition GUID
d display the sector alignment value
e relocate backup data structures to the end of the disk
g change disk GUID
h recompute CHS values in protective/hybrid MBR
i show detailed information on a partition
l set the sector alignment value
m return to main menu
n create a new protective MBR
o print protective MBR data
p print the partition table
q quit without saving changes
r recovery and transformation options (experts only)
s resize partition table
t transpose two partition table entries
u Replicate partition table on new device
v verify disk
w write table to disk and exit
z zap (destroy) GPT data structures and exit
? print this menu
Expert command (? for help): v
Caution: The CRC for the backup partition table is invalid. This table may
be corrupt. This program will automatically create a new backup partition
table when you save your partitions.
Caution: Partition 1 doesn't begin on a 8-sector boundary. This may
result in degraded performance on some modern (2009 and later) hard disks.
Caution: Partition 2 doesn't begin on a 8-sector boundary. This may
result in degraded performance on some modern (2009 and later) hard disks.
Caution: Partition 3 doesn't begin on a 8-sector boundary. This may
result in degraded performance on some modern (2009 and later) hard disks.
Consult http://www.ibm.com/developerworks/linux/library/l-4kb-sector-disks/
for information on disk alignment.
Identified 1 problems!
Expert command (? for help): x
a set attributes
c change partition GUID
d display the sector alignment value
e relocate backup data structures to the end of the disk
g change disk GUID
h recompute CHS values in protective/hybrid MBR
i show detailed information on a partition
l set the sector alignment value
m return to main menu
n create a new protective MBR
o print protective MBR data
p print the partition table
q quit without saving changes
r recovery and transformation options (experts only)
s resize partition table
t transpose two partition table entries
u Replicate partition table on new device
v verify disk
w write table to disk and exit
z zap (destroy) GPT data structures and exit
? print this menu
Expert command (? for help): p
Disk /dev/sda: 5860531055 sectors, 2.7 TiB
Logical sector size: 512 bytes
Disk identifier (GUID): 2D50CD70-85F5-46FE-85B3-35A027E3C828
Partition table holds up to 128 entries
First usable sector is 34, last usable sector is 5860531021
Partitions will be aligned on 8-sector boundaries
Total free space is 2957 sectors (1.4 MiB)
Number Start (sector) End (sector) Size Code Name
1 34 73658024 35.1 GiB EF00
2 73722285 5860528064 2.7 TiB FD00
3 73658025 73722284 31.4 MiB EF02
Expert command (? for help): w
Final checks complete. About to write GPT data. THIS WILL OVERWRITE EXISTING
PARTITIONS!!
Do you want to proceed? (Y/N): y
OK; writing new GUID partition table (GPT) to /dev/sda.
The operation has completed successfully.
root@ubuntu:/cdrom/HPA_recovery# gdisk /dev/sda
GPT fdisk (gdisk) version 0.8.8
Partition table scan:
MBR: protective
BSD: not present
APM: not present
GPT: present
Found valid GPT with protective MBR; using GPT.
Command (? for help): q
Mais uma vez, obrigado a todos por toda a ajuda.