I am facing something similar.  I am already struggling with an issue on this 
Tyan S3970 (Ubuntu 12.04.03 fully updated), which I am in the process of 
reporting here:
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1217229

I have a pair of system disks (raid/luks) which I am able to boot.  I
have a pair of data disks (raid) which, when attacked to the sata
controller (along with the system disks) lead to a boot failure and
drops me into busybox.  When I hit control-d to continue the boot, I get
stuff that looks like:

BUG: soft lockup - CUP#7 stuck for 23s! [kworker/7:0:469]
BUG: soft lockup - CUP#7 stuck for 22s! [kworker/7:0:469]
INFO: rcu_sched self-detected stall on CUP { 7} (t=15000 jiffies)
INFO: rcu_sched detected stalls on CPUs/tasks; { 7} (detected by 2, t=15004 
jiffies)
INFO: Stall ended before state dump start

I have posted pictures of my screen.  The first pic is of one boot.  The second 
pair is of a second boot, both using Ctl-D from busybox:
https://www.dropbox.com/sh/whypnvtkzkdyx3p/u3bnQQBqjb

One more piece of information: When I first booted with all 4 disks
attached (zero'th boot, if you like), I was successful.  I tried to
mount the data disks and got a degraded array.  That was odd, as I
checked and the disk health was reported as good/healthy for both disks.
Also, I had been watching the disks and there has been no sign of either
disk developing problems.  It's when I shut down and rebooted that I
found myself getting dropped into busybox and took the first picture.

More information on my machine is located at the above bug report.

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https://bugs.launchpad.net/bugs/1011914

Title:
  BUG: soft lockup - CPU#0 stuck for 23s! [kworker/0:3:566]; RIP:
  0010:[<ffffffffa00c9d73>] [<ffffffffa00c9d73>] mei_timer+0xc3/0x260
  [mei]

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