This issue was reported by Per Bothner. The following is from his email:

===== email =====
The general case of (integrating) a user-provided ScriptContext or Bindings object is painful. However, we can do better when using a ScriptEngine's default ScriptContext and Bindings.

Specifically, I suggest:

When in the NashornScriptEngine constructor), do:

  context.setBindings(new NashornBindings(globalObject), ScriptContext.ENGINE_SCOPE);

where:

/** A wrapper (proxy) for a ScriptObject viewed as a Map. */
class NashornBindings implements Bindings {
   ScriptObject base;
   public NashornBindings(ScriptObject base) { this.base = base; }
   public Object get(Object key) { return base.get(key); }
   ... other methods implementing Bindings using base ...
}

Every program that uses the default ScriptContext and Bindings (which I hope most so, and which we should encourage) now works much better, because the ScriptEngine's ENGINE_SCOPE is now automatically synchronized with the globalObject: The ScriptEngine evaluator automatically sees the properties of the globalObject, and JavaScript using the same Global automatically sees the bindings done by the ScriptEngine.