Hello Leo,
I thought I was the only one with this problem. I too have a JVC PRO HD 100 E Camera (PAL land) and I captured a one hour HDV tape using Premiere Pro 2. Like you it captured the whole hour but after conforming (Indexing) the first section of audio loops every 12 mins. I too downloaded the JVC Pro HD Presets from the Adobe website.
Leo have you had any luck in resolving this problem.?