For some reason latex-beamer-3.06-r1 ebuild doesn't install beamer.layout file for lyx, but I think it should.
Have you got app-office/lyx installed? I'm trying to reproduce... Can you post emerge --info?
I didn't have lyx installed when I had installed latex-beamer. I installed lyx after installing latex-beamer. I see the if has_version 'app-office/lyx' ; then section now. I should have looked at the ebuild before. Is that the correct gentoo way of doing things? I would think the correct way would be to use a lyx use flag? That was the first thing I checked actually, I did an emerge -vp latex-beamer to see if there was a lyx use flag that wasn't enabled. I think using has_version is hiding stuff from the user. Having the use flag allows one to do an emerge -uvaN world
I agree a lyx use would be better. Please see also bug #93730, comment 1.
You are right. I added a lyx-use-flag to latex-beamer-3.07.