I have seen many posts about how to obfuscate an Android application (.apk file) using ProGuard in Eclipse. Also see http://developer.android.com/guide/developing/tools/pro
Do not obfuscated your pure Java Jar. Skip that phase completely while producing the Jar (whether manually in Eclipse or via Ant build from command line).
Instead, setup and perform proper obfuscation in the client project, the one using the Jar, where you add the library as external Jar. Proguard will be able to obfuscate code within the Jar too.
I stumbled upon this issue, and ended up successfully as I described here.