I got exactly the same problem, on Ubuntu 10.04.1 64bit :

Did you find any workaround by tweaking the parameters in the 3ware BIOS ?
Could it be caused by the 64 bit system ?

# uname -a
Linux NAS 2.6.32-24-server #39-Ubuntu SMP Wed Jul 28 06:21:40 UTC 2010 x86_64 GNU/Linux

01:00.0 RAID bus controller: 3ware Inc 9650SE SATA-II RAID PCIe (rev 01)
        Subsystem: 3ware Inc 9650SE SATA-II RAID PCIe
        Flags: bus master, fast devsel, latency 0, IRQ 16
        Memory at f8000000 (64-bit, prefetchable) [size=32M]
        Memory at fbdff000 (64-bit, non-prefetchable) [size=4K]
        I/O ports at c800 [size=256]
        Expansion ROM at fbdc0000 [disabled] [size=128K]
        Capabilities: [40] Power Management version 2
        Capabilities: [50] Message Signalled Interrupts: Mask- 64bit+ Queue=0/5 Enable-
        Capabilities: [70] Express Legacy Endpoint, MSI 00
        Capabilities: [100] Advanced Error Reporting <?>
        Kernel driver in use: 3w-9xxx
        Kernel modules: 3w-9xxx

# dmesg | grep 3w
[    1.642150] 3ware 9000 Storage Controller device driver for Linux v2.26.02.012.
[    1.642186] 3w-9xxx 0000:01:00.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16
[    1.642190] 3w-9xxx 0000:01:00.0: setting latency timer to 64
[    2.719058] scsi4 : 3ware 9000 Storage Controller
[    2.719137] 3w-9xxx: scsi4: Found a 3ware 9000 Storage Controller at 0xfbdff000, IRQ: 16.
[    3.078989] 3w-9xxx: scsi4: Firmware FE9X 4.08.00.006, BIOS BE9X 4.08.00.001, Ports: 8.
[    4.390974] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.
[    4.391246] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.
[    4.391495] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.
[    4.427395] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.
[    4.429360] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.
[    4.429615] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.
[   93.437874] 3w-9xxx: scsi4: AEN: INFO (0x04:0x000C): Initialize started:unit=1.
[ 1215.126837] 3w-9xxx: scsi4: AEN: INFO (0x04:0x005E): Cache synchronization completed:unit=1.
[ 1226.366384] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.
[ 1226.382731] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.
[ 1236.209880] 3w-9xxx: scsi4: AEN: INFO (0x04:0x000C): Initialize started:unit=1.
[ 1236.495049] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.
[ 1236.495410] 3w-9xxx: scsi4: ERROR: (0x03:0x0101): Invalid command opcode:opcode=0x85.

I am also having dpkg hanging up, this was also during a heavy disk I/O (mkfs on a 6TB partition)  :

[ 2880.398449] INFO: task dpkg:1214 blocked for more than 120 seconds.
[ 2880.398522] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message.
[ 2880.398589] dpkg          D 0000000000000000     0  1214   1196 0x00000000
[ 2880.398596]  ffff88007ba83db8 0000000000000086 0000000000015bc0 0000000000015bc0
[ 2880.398603]  ffff880132269ab0 ffff88007ba83fd8 0000000000015bc0 ffff8801322696f0
[ 2880.398608]  0000000000015bc0 ffff88007ba83fd8 0000000000015bc0 ffff880132269ab0
[ 2880.398615] Call Trace:
[ 2880.398627]  [<ffffffff81166cb0>] ? bdi_sched_wait+0x0/0x20
[ 2880.398632]  [<ffffffff81166cbe>] bdi_sched_wait+0xe/0x20
[ 2880.398640]  [<ffffffff8155910f>] __wait_on_bit+0x5f/0x90
[ 2880.398644]  [<ffffffff81166cb0>] ? bdi_sched_wait+0x0/0x20
[ 2880.398650]  [<ffffffff815591b8>] out_of_line_wait_on_bit+0x78/0x90
[ 2880.398658]  [<ffffffff810850d0>] ? wake_bit_function+0x0/0x40
[ 2880.398662]  [<ffffffff81166c74>] ? bdi_queue_work+0xa4/0xe0
[ 2880.398668]  [<ffffffff8116801f>] bdi_sync_writeback+0x6f/0x80
[ 2880.398673]  [<ffffffff81168050>] sync_inodes_sb+0x20/0x30
[ 2880.398678]  [<ffffffff8116bbc2>] __sync_filesystem+0x82/0x90
[ 2880.398683]  [<ffffffff8116bca9>] sync_filesystems+0xd9/0x130
[ 2880.398688]  [<ffffffff8116bd61>] sys_sync+0x21/0x40
[ 2880.398696]  [<ffffffff810131b2>] system_call_fastpath+0x16/0x1b