In my experience, the DTS-HD tracks we use around here aren’t possible to get working with seamless branching. Many software packages report the wrong run times on those files, for whatever reason, and their compatibility seems somewhat limited. But it is possible that Williarob will have better luck.
(this is why my seamless branching disc just has the dolby digital tracks instead).
Has anyone tried simply reencoding them? DTS-HD is lossless, after all, so you won’t be losing anything. But you might gain some well-behaved files as a result. Or is it DTS-HD itself that has compatibility issues?