I've tried re-encoding and it doesn't seem to have fixed the issue. I'm using encoding.com and have tried using similar settings as described here (at least the ones which look like they could make a difference): http://www.encoding.com/using_wowza_media_server
My settings for an example encode are:
It just seems weird that I can play the files fine using a player like mplayer, but Wowza seems to have a problem with the video. There doesn't seem to be any problem with other videos I have encoded so I'm not sure what the best next step is to debug this and get it working, and to avoid running into this problem again in the future (or at least know how to troubleshoot)?