Please upgrade to apt version 0.6.46.4ubuntu6 and see if it still does
it. onc eyou remove the bin files from /var/cache/apt/ leave them
deleted and it should work fine. the .bin files were getting corrupted
but this issue has been fix in feisty.

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apt segmentation faults (core dump) in feisty
https://launchpad.net/bugs/72475

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