Happy to help figure this out.
Can you describe your setup in more detail? Describe your source stream: encoder make/model, codecs, bitrate, resolution, keyframe interval, etc… A keyframe interval of 2 sec is recommended.
Can you post your transcoder template? FYI, you can encode large bits of text in BB code brackets, for readability.
Have you done any troubleshooting, such as sending a low complexity stream and using a transcoder template with just two total transcoded streams? Any error messages, or pattern you notice?
If you don’t get it sorted, it will help if you can provide steps to reproduce.