I was making another video and in one scene I had to speed up the dialog to fit. I used speed/duration and increased the speed to about 115%, and checked off the box to not affect the pitch. It plays back in Premiere Pro but when I encode the entire video with AME, that one scene is silent. I'm currently trying to encode it with Premiere Pro rather than AME but I don't know yet if that will do the trick.
Thanks Chris. Turns out the faster workaround was to export with Premiere Pro. Luckily it was only a 34 second video. Seems to be a similar problem to AME repeating the last second of audio at the end of a sequence. They say they fixed that in cc 2016. Hopefully they can fix this bug with an update, although I doubt the situation comes up much.