I had the same problem myself with my old tracks I imported before RB 2.0.1. But its a very easy fix ;) You have to mark the tracks you want to auto load hotcue, then click on the Info tab or Property if you right click. In the right corner of the Info you will se Allow to auto load HotCue on CDJ. Mark it and the tracks you selected will auto load hotcue :)
Hope this helps :)