Bug 104594 shows the error produced due to media-gfx/kst-1.1.0 silently detecting and linking to netcdf, and there being no shared library to link to. This results in a failure to compile on systems with netcdf installed on PIC sensitive architectures. It also breaks reverse dependencies of kst-1.1.0 as it is linking against netcdf when present without any DEPEND in the ebuild. A quick look at the ./configure --help seems to indicate no enable/disable of this feature - just a switch to specify lib location. This blocks kst-1.1.0 being stabilised on amd64 until the issue is resolved.
Adding media-gfx/kst-1.1.0-r1 to portage with a patched configure which prevents unconditional linking to netcdf. Thanks to Lucas Chiesa <lucas.chiesa@gmail.com> for providing the patch.