>> This critical thread is at RR priority 50.

Try to put it higher than the irq thread handling your HD hardware.
I've even encountered hardware where I had to put the ATA thread
in the SHED_OTHER domain - see [1] for the thread.

>> I used a HR timer thread with RR pri 55 to wakeup the critical thread
>> every 1 milli sec to do the job.

Which prio is the ksoftirqd running at? The HRTIMER interrupts are
routed through it so it also has to be high enough.

I got burned with this myself [2]

Regards
                                     Stano

[1] http://www.spinics.net/lists/linux-rt-users/msg08711.html
[2] http://www.spinics.net/lists/linux-rt-users/msg08745.html

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