Create PDF from Web page using Acrobat X - Page Order

I have a structured web site that is in fact Program Help The web pages are structured as follows:
index.html - Main Topic Index page with links to all topic subject index pages
topic/index.html - Topic Subject Index Page with links to all subject pages
topic/subject.html - Subject page
.....etc
Using Acrobat 5 "Create PDF from Web Page" created a perfect logical PDF  page structure in the page order of of the web site. In Acrobat 5 page 1  was the Main Topic Index Page, page 2 was the 1st Topic Subject Index  Page, page 3 was the 1st Subject Page, then the 2nd subject of the 1st  Topic, etc. until the Topic Subjects were exhausted after which the 2nd  Topic Subject Index Page and so it went on. As a result the bookmark  structure was sensible. The page order was as follows:
Main Topic Contents
Topic 1 Contents
Subject 1 of Topic 1
Subject 2 of Topic 1
Topic N Contents
Subject 1 of Topic N
Subject 2 of Topic N
Acrobat X (just purchased) produces a differently structured PDF from the same HTML pages. The order is:
Main Topic Contents
Topic 1 Contents
Topic 2 Contents
Topic N Contents
Main Topic Contents (a second time)
Subject 1 of Topic 1
Subject 2 of Topic 1
Subject N of Topic 1
Subject 1 of Topic 2
Subject 2 of Topic 2
Subject N of Topic N
Question: Is there any way I can get back with Acrobat X the same page order I got with Acrobat 5?
Any help appreciated. The website is www.caliach.com/caliach/vision/help/index.html
Chris

Acrobat is using the underlying mark up of the rendered HTML page.
This may or may not provide an adequate input to Acrobat when it is noodling out how and what to tag.
I suspect you may find that, to obtain an adequately tagged PDF, you may have to capture the web page content with the create bookmarks and create tags options off.
Once you have the PDF make working copies.
Try letting Acrobat tag this already created PDF to see what happens.
You may have to manually tag the PDF.
n.b., The default read order for western language can be altered by user selections in the accesibility setup or by selection in the PDF page(s) Page Properties.
Be well...

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