Are you using htree? Run
dumpe2fs -h /dev/hda1 | grep features
and if it says "dir_index" then try turning it off:
tune2fs -O ^dir_index /dev/hda1
and reboot.
If it is not an htree problem (and htree seems pretty stable now) then
possibly the IO system has lost some data. If possible, try using a normal
old disk (no RAID).
Falling back to ext2 for a while would be interesting.
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