Encore 2.0 automatically adds a hidden chapter point at the end of every timeline...it's a feature.
Its purpose is to execute the timeline end action so reliable navigation is provided, reason being that many DVD players execute a title search when you hit the Next button, which before Encore 2.0 would then bring you to the next title on the DVD. Many times, this would result in undesirable navigation behavior (and users would have to add a chapter point manually to the end of a timeline), hence the new feature.
Some burning applications may not correctly handle this new feature. If yours does not, then build a DVD image in Encore 2.0 (this creates the entire disc structure) and then burn the image from your burning application. The behavior should be the same as burning directly from Encore.