I have just installed Gentoo from 2006.0 livecd. First of all, all changes to make.conf file are ignored. I change USE/SYNC flags in it, but emerge --info doesn't take it into account env-update && source /etc/profile doesn't help I found dirty patch to it - added "source /etc/make.conf" line to the /etc/profile file. Yeah, I know it shouldn't contain any reference to make.conf, this is why it not a "Gentoo Way" to solve the problem. As far as I know, it's quite "popular" problem (I found 4 topics at forums.gentoo.org with the same problem). After that I tried to "emerge system", but it failed 'cos pam-login is blockin' shadow (>=shadow-4.0.14-r2) and vice-versa.
For the pam-login/shadow block, unmerge pam-login and immediately after that emerge shadow with the pam USE flag.
Wrt your make.conf issue, emerge --info missing here. Also, some steps to reproduce the problem are needed. Works just fine here, referring to some unspecified topics on forums is not useful at all. (For pam/shadow blockers, see Bug 126014, it's not a bug at all).
