I saw this one one of my own machines and only one machine.
The configuration stage can potentially call autoconf which causes issues with the configure script as it includes options that do not exist and the configure bombs.
Fix will be applied shortly.
This issue was caused by the fix for Issue #1 but did not occur on all machines.
The solution was to add src_configure to all ebuilds and transfer the configuration into that ebuild sub.
I saw this one one of my own machines and only one machine. The configuration stage can potentially call autoconf which causes issues with the configure script as it includes options that do not exist and the configure bombs. Fix will be applied shortly.