I also had this issue but I can't really nail it down. The explanation
that it has only something to do with Kernel 2.6.32-rc* makes sense. I
used it several times on my two systems. I got different md5 for the
same file and if I played a video which was affected the player stops
and the hard disks runs all the time and the systems hangs for a minute
or more. It looks like a part was missing and the driver was searching
for it.

I even shot down my whole testing system. I have a small testing partition to 
test Linux outside the VM. After some xorg edgers installation and restart I 
got an fsck problem which asks for confirmation, some inode problem. After 
confirmation it asks again several times so I run it with -y which delete a lot 
of files. Afterwards the system didn't boot anymore.
I have installed grub on the partition instead of the MBR, maybe that resulted 
under some special circumstances in this problem but I have done this since a 
long time and never had problem with it.

So actually using of 2.6.32 makes more sense since I use ext4 since
quite some time. I haven't had a problem since sticking with the default
Kernel but this problems doesn't just pop up. You don't realize that a
huge file has changed until actually checking/using the whole thing.

-- 
corruption of large files reported with linux 2.6.31-14.46 on ext4
https://bugs.launchpad.net/bugs/453579
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