Some symlinks were moved from texlive-bin to texlive-htmlxml, -langgreek, -langextra, -pictures, -pstricks, and -science, where they actually belong (see FS#16037). One of them was unfortunately omitted, due to a typo in the PKGBUILD, so there is a conflicting file in texlive-bin and texlive-langgreek. The solution is to force overwriting /usr/bin/mkgrkindex.
TeXLive update issue
2009-09-11 - François Charette