Local ref garbage collection within "nested" JNI calls

Question

I am using a JVM started in C++ to make calls to java classes. The C++ code makes JNI call into the JVM which instantiates a java class. The java class, in the course of execution, makes other JNI calls. All this happens on one thread of execution.
What I am seeing is that local references from the native methods being called by the java class are not being released until the initial C++ native call exits. The JNI spec (text included below) seems to indicate there is registry of "nonmovable local references to Java objects" which "keeps the objects from being garbage collected". Is there only one such registry which does not get deleted until the initial C++ native call exits? If so, this would explain what I am seeing. How do I get around it?
Thanks,
Iztok
From the JNI spec:
"To implement local references, the Java VM creates a registry for each
transition of control from Java to a native method. A registry maps nonmovable local references to Java objects, and keeps the objects from being garbage collected. All Java objects passed to the native method (including those that are returned as the results of JNI function calls) are automatically added to the registry. The registry is deleted after the native method returns, allowing all of its entries to be garbage collected."

Answer 1

When I say "initial" I mean the initial C++ JNI call into a JVM running in a C++ process as shown in the pseudo code below. initNativeFunc() makes a call to Foo.doSomething() function which calls nativeFunc2 (another native function). Only a local reference to Retval was created in nativeFunct2, so when nativeFunct2 returns and the Retval is no longer used in Foo it should be a candidate for garbage collection. But this is not what happens. The Retval from nativeFunc2 is not being cleaned up until Foo.doSomething() returns. If I make the loop in Foo.doSomething() long enough, NewDoubleArray() returns a NULL when it runs out of memory.
void initNativeFunc() {
jclass clazz = env->FindClass("Foo");
jmethodID mid = env->GetMethodID(clazz, "doSomething", "()V");
env->CallVoidMethod(clazz, mid, ...);
JNIEXPORT jobject JNICALL nativeFunc2() {
jclass clazz = env->FindClass("Retval");
jmethodID mid = env->GetMethodID("Retval, "<init>", "()V");
jobject retval= env->NewObject(clazz, mid);
jdoubleArray da = env->NewDoubleArray(100000);
jfieldID fid = ...
env->SetObjectField(retval, fid, da);
return retval;
public class Foo {
public native void nativeFunc2();
public void doSomething() {
for (int i = 0; i < 100; i++) {
Retval retval = nativeFunc2();
}