Yes the menuing is not the best.
Seeing as you have
Nero Vision (I use NeroVision Express 3 from version 6) you can use that to finish your project. You would 'Add' the resultant VOBs from
ConvertX, create some chapters and make your menu. As long as you have 'Smart Encoding' enabled Nero won't re-encode. It should take about ½ hour to do. Save to your HD so you can check the results before committing to disc.