I had the same issue today. It seems like live playback is broken in the current version of JW Player. I am also having problems with video on demand playback as well (stutters for 2 seconds at the start). I suggest installing JW Player 4.x for now until it gets resolved:
http://community.wowza.com/t/-/33
I have sent a message to the JW Player folks to make sure we get this resolved quickly.
Charlie