Calling stop() on a playing AudioClip takes a long time -- roughly 20-30 milliseconds, enough to cause a visual stutter in an app that updates at 60 fps (via an AnimationTimer).

There is no delay or lag if an AudioClip finishes playing on its own.

I have created a test app which measures the lag:
http://electronzen.com/AudioClipTest/

Launch the app. Press Play to start the clip. Press Stop when the clip is playing to see the frame time delta jump.