I have a system exhibiting the same/similar symptoms.

Running a fresh install of Ubuntu 9.04 jaunty
uname -a: Linux ServerX 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:58:03 
UTC 2009 x86_64 GNU/Linux

Motherboard: SUPERMICRO MBD-H8DME-2-O
SATA card: SUPERMICRO AOC-SAT2-MV8 (Marvell Technology Group Ltd. MV88SX6081 
8-port SATA II PCI-X Controller (rev 09))

The system has a SW RAID6 array made of four 1TB disks. Currently the
array is degraded and only has 3 disks to work with.

md1 : active raid6 sde1[4] sdd1[0] sdc1[2]
      1953519872 blocks level 6, 64k chunk, algorithm 2 [4/2] [U_U_]
      [==>..................]  recovery = 10.8% (105874700/976759936) 
finish=142.0min speed=102195K/sec

With the array on the PCI-X card I'm able to recreate the crash by
failing a drive and reading it to the array. Some time after 50% it will
hang and the system is unresponsive.

The system boots from RAID1 md0 two 500GB drive which is on the
motherboards controller. I was able to add a disk plugged into the PCI-X
to md0 and it would sync w/o problems.

Moving the RAID6 array to the mother boards controller the rebuild will
work w/o problems.

kpolberg mentioned adjusting stripe_cache_size.The command he posted:
      echo 16384 > /sys/block/md1/md/stripe_cache_size
Looks like it helps, no crash fro 24Hrs.

If it remains stable I will try with a larger array.

Will post more info if needed.

-- 
mdadm with Raid5 stuck in uninterruptable sleep
https://bugs.launchpad.net/bugs/208551
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