version 1.17 of the make.defaults file in the 2006.0 AMD 64 profile seems to have mistakenly included a whole bunch of use flags, and is no longer setting nptl. The offending commit is here http://www.gentoo.org/cgi-bin/viewcvs.cgi/profiles/default-linux/amd64/2006.0/make.defaults?r1=1.16&r2=1.17.
fixed in cvs, sorry about that.