When doing an emerge and the package is masked by ~amd64 it doesn't printout that the package belongs to an overlay.
Example of a problem.
$ sudo emerge libwnck -pv
!!! All ebuilds that could satisfy "libwnck" have been masked.
!!! One of the following masked packages is required to complete your request:
- x11-libs/libwnck-2.16.2 (masked by: ~amd64 keyword)
- x11-libs/libwnck-2.16.1 (masked by: ~amd64 keyword)
- x11-libs/libwnck-2.14.2 (masked by: ~amd64 keyword)
For more information, see MASKED PACKAGES section in the emerge man page or
refer to the Gentoo Handbook.
$ cat /usr/portage/x11-libs/libwnck/libwnck-2.16.2.ebuild | grep KEYWORDS
KEYWORDS="~alpha amd64 ~arm ~hppa ~ia64 ppc ppc64 ~sh sparc x86"
$ sudo env ACCEPT_KEYWORDS="~amd64" emerge libwnck -pv
These are the packages that would be merged, in order:
Calculating dependencies... done!
[ebuild N ] x11-libs/libwnck-2.16.2 USE="-debug -doc" 0 kB 
Total size of downloads: 0 kB