Absolutely: test a build and do not rely on the Encore preview.
VLC has improved, and provides good test. I have not found WMP to be better. I only rely on Total Media Theater 5 or 6. This is primarily due to it being more reliable with difficult to emulate processes such as slideshows. (I don't use Encore slideshows, but it was my acid test for an emulator.) I would not worry about your results, because I think the problems you are seeing reflect actual problems in your project.
I cannot tell from your description what your navigation problems are (or not). I do think you will be better served to use playlists and chapter playlists and and to avoid overrides.