To create a functional ISO, here's what I end-up doing:
1. Burn directly to a Blu-Ray disc via PE13
2. Open ImgBurn
3. Select 'Create image from disc'
4. You get prompted that you need to use "Build" mode to create a Blu-ray image
5. Use Build mode to manually add the two directories on the disc to the image
6. Start
I can then use this ISO to burn additional discs with no problem.
A lot of work to create something that PE13 should be doing correctly on its own.