From the look of it, encore CS6 (the newest one available) is not compatible with compositions from after effects cc 2015.
More specifically, as an animated menu.
Render the file using the Lossless with alpha preset for the output module. The only change I would make would be to change the color mode from Premultiplied to Straight. That will give you exactly the same results as importing a project using Encore's dynamic link only it will render and compile faster in Encore than an AE comp would.
This works nicely, I assumed that I would add it to the flowchart before the menu.
There is a black frame between the end of the rendered file and the menu but I can live with that for this project.
Thanks for your help.