This to me sounds more like an encoder issue. What is the cpu and memory load on the encoder machine for each of these cases:
1.SD Cam(480i)30fps–>WireCast3.5.2 1Mb/s640*480(RTMP)H.264 -->WowzaPro1.7Live–>Flash10 Good! 30fps.
2.SD Cam(480i)30fps–>WireCast3.5.2 1Mb/s640*480(RTP)H.264 -->WowzaPro1.7Live–>Flash10 Good! 30fps.
3.HD Cam(720P)30fps–>WireCast3.5.2 1Mb/s640*360(RTMP)H.264 -->WowzaPro1.7Live–>Flash10 Not good! Movie is Slow motion.
4.HD Cam(720P)30fps–>WireCast3.5.2 1Mb/s640*360(RTP)H.264 -->WowzaPro1.7Live–>Flash10 Not good!! 1fps #.
Wowza Pro does not really touch the video/audio packets. We simply relay them to the player. So we are not directly affected by the frame size. These types of issues are more likely on the encoder or Flash player side of things.
Charlie