etc-update uses /tmp/$$ vs $PORTAGE_TMPDIR For security reasons when etc-update is first run it deletes /tmp/$$. If another process is using /tmp/$$ for legit reasons etc-update will kill it off.
Created attachment 59834 [details, diff] etc-update-tmpdir.patch patch that updates behavior.
Fixed on or before 2.0.51.22-r1
Looking through the batch of bugs, I'm not sure that some of these are actually fixed in stable. Others, the requirements have possibly changed after the initial fix was committed. If you think this bug has been closed incorrectly, please reopen or ask that it be reopened.