18:41:21: Scene buffering time set to 400
Set this to 700 instead of 400.
Set this to yes instead of no (i.e. turn Constant Frame Rate on).
18:44:53: PERFORMANCE WARNING: Scene change took 1946 ms, maybe some sources should be global sources?
Try following this advice.
18:45:35: RTMPPublisher::SocketLoop: Stalled for 4078 ms to write 333704 bytes (buffer: 0 / 335872), unstable connection?
18:45:44: RTMPPublisher::SocketLoop: Stalled for 9202 ms to write 335800 bytes (buffer: 0 / 335872), unstable connection?
Some indication here that your internet connection is congested. Eliminate other things that might be sharing the connection, or lower your bitrate, or worry about your ISP.
20:07:43: Total frames encoded: 155448, total frames duplicated: 5104 (3.28%)
20:07:43: Number of frames skipped due to encoder lag: 1392 (0.90%)
20:07:43: Total frames rendered: 153122, number of late frames: 591 (0.39%) (it's okay for some frames to be late)
Your CPU isn't keeping up for some reason, based on the way-too-high duplicated frame percentage. I'm hoping after making the changes above it'll drop to under 1%.