I 've had this problem berfore. I build an HD project in Premiere Pro CS4 with 20 chapters (and Yes they are Encore Chapter Markers). I open Encore CS4 and use Dynamic Link to import the project and I create a timeline but the timeline has no chapters. I do this all the time and it works perfectly but once in a while this happens. I tried right clicking on the timeline and selecting Update Markers from Source. I tried reopening the PPro project, saving it as another name and starting from scratch in Encore but still no chapters.
Not only have I never named them, I have never seen an option to name them, yet they have always worked without naming them for 4 years.
Upate: All my projects are on removable hard drives. So I just opened this one in another computer. And again, no chapters.
Try naming them in the affected sequence just to see if it makes a difference in this instance.
Also, please confirm dynamic link, and that the sequence has not been transcoded.
I might be able to test with CS4 tomorrow.
I did not transcode anything yet. I reopened the Ppro project, double clciked on 5 of the Encore markers, named them and saved and closed the project. I opened Encore, created a new project, dynamically linked the nedwPpro project, created a timeline and again, no chapters.