Hello,
I recently faced a similar one in my company, the issue was the new antivirus.
Has been discovered only for some few packages and so after a clean rebuild 
(that has required t ore downloaded every packages). Errors were on do_fetch 
and do_unpack depending of the packages.
Not sure it's related to your issue, but my be something to check.
I'm using kirkstone 4.0.10 actually.
Joel
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