OK, tried again with the new version. Now the problematic tracks look like this:
The subs in the last scene are still wrong, their length should be equal to the scene duration (no Stop), same for the highlight layer. I do have the buttons in this menu now, but they won't highlight anymore after some seconds, of course.
The issue with FieldDeinterlace() added to the AVS scripts no matter what is fixed. Alternate scan and pause for script verification is fixed too, but just noticed that "Copy Remaining Menu Files" setting isn't saved.
EDIT: during CCE encoding, my taskbar is locked at times (Windows XP). Clicking something in the taskbar/tray doesn't do anything, eventually things will pop up all of a sudden some time later.
Thanks!