I was able to create an HD DVD using the default "Best Automatic" setting using some of the clips that were problematic before, and the disc plays in both a Toshiba standalone HD DVD player and in Apple's DVD Player application. However, I was still unable to create the same disc using a custom 20 Mbps H.264 encoding setting. With this setting, the disc creation fails with a -50 Error. The discs that do work still don't work in my Xbox 360 HD DVD drive, as I cannot navigate beyond the menu on that player. However, as I mentioned before, this may in part be due to the player itself.
Apparently some of the Blu-ray problems have been fixed too. Roxio states that Toast 9.0.2:
* Resolves a number of encoding issues related to high-definition source content and creation of Blu-ray video discsHowever, I have not yet tested Blu-ray creation as I do not own a Blu-ray player, and Apple's DVD Player does not support Blu-ray.
* Resolves situation where high-definition DVDs would not play back on PlayStation 3