The original JNI book says that ExceptionDescribe has the side effect of clearing the exception
This text is not present in the on-line JNI specification
However hotspot most certainly does clear it as I see this :-

JNI_ENTRY_NO_PRESERVE(void, jni_ExceptionDescribe(JNIEnv *env))
JNIWrapper("ExceptionDescribe");

HOTSPOT_JNI_EXCEPTIONDESCRIBE_ENTRY(env);

if (thread->has_pending_exception()) {
Handle ex(thread, thread->pending_exception());
thread->clear_pending_exception();
....

and a small test progam I wrote confirms that behaviour.