Wowza is pretty particular about how and where it will stream... Doesn't matter how much you spent on your encoding software. FFmpeg conversion was how I typically corrected mp4 files for streaming whenever issues popped up. Look carefully at what flags you are using as well with ffmpeg.
You also might want to check around for notes on the specific version of JWplayer since you are using that as your video container. Some of the newer versions believe it or not we're showing some pretty heavy incompatibilities with wowza streaming out of box, while older versions worked fine. I'm on ICQ after this weekend, or email if you'd like a second set of experienced eyes on the issues.
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“ I have the simplest tastes. I am always satisfied with the best.” -Oscar Wilde
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