I also have the same issue. The only temporary solution I've found is rebuilding all the package dependencies with xcodebuild for x86_64 in run script build phases, but that's far from ideal. I really hope that there will be an option for somehow setting the target architecture for the compilation of the packages also, at least when building for simulator.

Thanks, but Software Update says that I'm up to date, even if I refresh it. That's why I don't know what to do. If I'm really not up to date how can I upgrade in this case?