Not sure what is going on, then. Putting the keystore file in your project’s Build/Android directory and just putting the name of the file into the project settings (NO PATH) is all you should need along with the key alias and password(s). After packaging you should see everything from Build/Android was copied to the project’s Intermediate/Android/APK directory which is where it is read from by Ant during the APK signing step.
I can’t reproduce the issue here.