The initial make.conf contains a deprecated "mcpu" command line switch in CFLAGS and CPPFLAGS. Currently it only causes the compiler to report a warning about '"mcpu" is deprecated, use "march" or "mtune" instead' at every file rebuild but when "mcpu" is dropped from the compiler, every ebuild will fail due a unrecognized compiler option.
Which tarball? Are you using the installer?
> Which tarball? stage1-x86-2006.0.tar.bz2 (and possibly stage2-x86-2006.0.tar.bz2 and stage3-x86-2006.0.tar.bz2 too as you are creating them from the stage1-x86-2006.0.tar.bz2) > Are you using the installer? No. But it might be affected too (if it only extracts the tarball to /, the flawed defaul make.conf is placed into /etc, if the user doesn't edit it but tries to compile anything using portage, this bug will appear).
OK. This was done on purpose. The reason is because the seed stage used to build the stage1 tarball was gcc 3.3 and the stage1 is 3.4... If you use stage2 or stage3, as recommended by the Handbook, then it is using -mtune instead. Also, this will "go away" on the next release simply because we'll be using a gcc 3.4-based seed stage. Basically, it isn't a "bug" per se, as it was done on purpose due to being required to build the release.
I'm using the 2006.0 minimal live CD for x86 and downloaded a stage 3 tarball and also get warnings about mcpu been deprecated because I copied /etc/make.conf.example to /etc/make.conf to get the nicely commented file
FIXED in 2006.1's release.