So I checked the Encore timeline for gaps; there were none.
I checked to see if a clip was shorter than it should be from another clipoverlapping it; no dice.
I removed all the clips and put them in again; nope.
I checked the Premiere timeline that I am using for the audio for gaps in the video: none there.
I droppped a two-channel wav file into the Encore timeline to see if that went out of sync; it did.
This last one I do not understand. In Premiere, my nested clips have the audio and video linked to each other so they cannot be placed out of sync. Running through the Premiere Timeline shows that the movie stays in sync the entire time.
One thing I did notice is that in Premeiere, in the Export settings window, The entire timeline is 1:49:16 and 50 frames, but in Encore it's 1:49:17 and zero frames. Then I realized that the Encore timeline is set to 29.97fps, as are the video clips I am dropping into it. But the Premiere timeline that I am using to export the audio was set to 59.94fps. So I made a new Premiere timeline set to 29.97fps, rendered the audio out again and placed it in Encore. Still falling out of sync. Tried with a two-channel wav file again, same problem.
I even tried just pasting the audio tracks into a new premiere sequence and exporting that, but that doesn't work either. That actually made things worse.For some reason the video is playing faster than the audio. At the beginning things are fine, but when you get to the end of the timeline, things are noticably out of sync. It's gradual, so there is no one spot that is causing a problem.
How do I fix this?