I'm not sure why the JARs installed by the proguard ebuild are split even more than they are upstream. That's not a problem but the way they are currently built results in most of the classes appearing in all of the JARs. There are also files missing from the ant and wtk JARs. Here's an ebuild that fixes all that.
Created attachment 197127 [details] proguard-4.3-r1.ebuild
Ebuild for proguard-4.4 now uses upstream build.xml so the extra files should be included and class duplication avoided.