So, please check where these files came from by

qfile /usr/src/linux-2.6.31-gentoo-r6/Makefile

WALRUS ~ # qfile /usr/src/linux-2.6.31-gentoo-r6/Makefile
sys-kernel/-MERGING-gentoo-sources (/usr/src/linux-2.6.31-gentoo-r6/Makefile)

Whatever that means.

Have you installed this kernel 'by hand' i.e. outside of portage?

No. I've not built nor installed *any* 2.6.31 kernel. I've never succeeded in emerging the sources.

Helmut, thanks for your rapid attention!