A mod may move this to the Encore forum.
Be sure you "run as administrator" for dual layer projects.
Encore may set the layer break correctly if it finds a good place, but there are numerous complaints about it being unreliable.
Build to a folder (no layer break is set), then use ImgBurn to build and ask to be prompted for layer break. ImgBurn is also unreliable under some circumstances.
The most frequent problems appear to be when there is no good location for a break. Do a search for "layer break imgburn" and you will see a variety of strategies.
Also see these posts:
Jon Geddes and Neil Wilkes