I wrote the Calibre version of the X-Ray generator - not the original web version - which was a bit foolish of me, since I don't actually have a newer Kindle which supports X-Ray, so I can't actually tell if it works or not.
But now I guess there are probably more X-Ray-capable Kindles around, so hopefully someone who has one can help out a bit.
What would be really useful is if someone could was able to:
1. get an official X-Ray file for a book (are there any free books with X-Ray data?)
2. generate a X-Ray file for the same book from the web version, or the Calibre plug-in
3. post them somewhere for comparison
That might help to nail down the problems. Since (AFAIK) there's no officially published file format it's hard to work out what's wrong.