You did not provide a conversion log.
Because you mentioned Chapters, I will assume you are using v3 ßeta right ?
Chapters are in the Root Menu, so if you use [B][X] Skip Root Menu[/B] will not see the root menu, unless you press the “Menu” button on your remote control.
Since the “Title Menu” is the menu where you select your videos, then goes directly to the video if you skip the root menu.
With [B][ ] Skip Root Menu[/B] when selecting a video, you will be shown the root menu, for that video.