I don't see any problem with etckeeper when I use the dialog frontend and upgrade with aptitude, which seems to be the configuration described in this bug report.
It sounds like whiptail isn't able to find a controlling terminal, which is strange, since aptitude shouldn't work at all without a controlling terminal. Please send either enough information to reproduce this problem, or a complete log (taken using script) from the shell prompt to the problem. -- see shy jo
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