I remember one thing that fixed several of my issues. It was to make sure that all audio tracks and video tracks are created at the exact same length.
For example, lets say your audio has one extra second of silence before the video starts. If you trim the audio in the timeline to match the picture, it messes up Encore. It’s better to take the track out of the program, fix it, and bring it back in.
Trimming audio and video exactly the same way seems okay, however. For example, if you want to trim one second from the top of both the audio AND the video on all tracks, that’s fine. If one track is trimmed differently than any of the others then problems start.
Hope that helps,
Bryan