Cosmetic and finicky, I know. I just noticed the ebuild for junit uses unzip to unpack, and I didn't happen to have unzip emerged so it failed (naturally, emerge unzip and the problem is gone.) I don't know if this problem exists with other packages, mostly because almost all the other packages are tgz or tbz2, but if an ebuild requires a certain archiver to unpack the distfiles, it should probably be considered to depend on that. That being said though, there's another way around. Junit depends on java, and java has 'jar', which can unpack zip files. Nuff said I guess.
Fixed. Ebuild commited to portage tree.