There's not much to go on here. You'll have to provide more info. See
here for guidelines on submitting a support request, which is also useful for posting to the forums.
Help us narrow down the problem. You're talking about streaming RTMPT from Wowza to a Flash player, correct? How does RTMP look with the same media? What is the stream/file encoding? How is your CPU/network load?
That is one of the example clients that ship with Wowza, a Flash application. The encoder is built into the Flash plug-in. It can't be compared to FMLE or any dedicated encoder, it is much more limited.