Lets bundle them and see what is already fixed in the new ebuilds.
I will look through existing bugs, add them here and lastrite sci-libs/(lapack/blas)-atlas.
The new package lives currently in the sci overlay and is named
# Justin Lecher <firstname.lastname@example.org> (5 Dec 2012)
# sci-libs/(lapack/blas)-altas will be removed due to
# fragile build and runtime behaviour #372323.
# Alternatives are sci-libs/lapack-reference & sci-libs/blas-reference.
# Follow up package named sci-libs/atlas can be found in
# sci overlay and will be moved once ready for prime time
Dropped all atlas packages from tree.
Please use sci-libs/atlas from sci overlay.
If problem still exist with that package, please reopen the bug or file a new one.