Ok, this might be a "duh", but I thought I'd share anyway . . .
If you use dynamic link to link a sequence between Premiere and Encore, and Premiere
was using MPE then Encore will also use MPE when it transcodes that sequence. There is no option
in Encore to switch MPE on/off. But, if you turn MPE off in the linked Premiere project it will also be off
in Encore. I discovered this because I was having Encore crashes and traced it back to an MPE issue.
In my case I had created a new Encore project and imported a Premiere sequence.
It makes sense. Dynamic Link means the linked asset is using a non-GUI version of the host app for playback.