After JNI ExceptionClear is called to clear a pending exception, JVMTI thinks the exception is still pending. JVMTI will not post an exception catch event, and future method exit and pop frame events will be reported as being caused by an exception.
This problem was introduced in 5.0 and was fixed in 5.0_03 by the fix for
6181784 Step requests ignored after an exception in debugee
It was accidently re-introduced in 6.