See bug 12698 and bug 12699 for the context that led to this report.
During bootstrap, the make.conf file is replaced with a bare-bones copy. This
is what caused me to stop the first pass; I add my own rsync and mirror URLs
to the make.conf so all downloads happen off my internal mirror. These are
lost during bootstrap.
To fix this, I ended up suspending the process (ouch, given problems reported
in bug 12698) and changed the make.conf so all but the first file were
downloaded from my site. Painful hack, but it made the downloads much faster -
gcc, glibc, etc. do not come in small tarballs.
Yes, we do need some fixes in the bootstrap script to fix these issues.
This is a duplicate of bug 662, which was marked fixed a while back. :)
This should now be fixed as we now grab the GENTOO_MIRRORS setting and in general better handle the make.conf backup.