I too have seen these corrupted files on amd64.  If you look at the end
of those files you'll see they end abruptly part way through the XML.
I've found the answer is to `sudo scrollkeeper-rebuilddb -v'.  This
deletes the whole database and re-builds it from scratch.  The problem
is that scrollkeeper-update, which it uses, clearly has memory
corruption problems so you have to keep doing the rebuild until it gets
to the end without crashing.

** Changed in: scrollkeeper (Ubuntu)
       Status: New => Confirmed

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Errors from scrollkeeper during updates from gutsy-{security,updates}
https://bugs.launchpad.net/bugs/158901
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