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Have you tried this?
Expand your Single Source Layouts pseudo folder
Right-click the WebHelp layout and click Properties
Click the Next > button twice
Note the option setting for "Optimize speed for". My guess is that it is set for "Web Site (Internet). If so, set it for "Local PC".
What normally happens is that when this setting is set for Web Site, the TOC/Index/Search/Glossary are split up into smaller (and hopefully more easily shipped) chunks. But this can have an adverse effect on synchronization. For example, let's say you click a link to a topic. The topic tries to sync, but that particular segment of the TOC hasn't yet been shipped. So the sync fails. By setting the option for Local PC, the navigation is kept in a single file. The trade off (there is always a trade off, eh?) is that it may initially take a bit longer for the TOC to display. But it should correct synchronization issues.
Thanks for your reply.
I actually use WebHelp Pro (with RE) so don't have this option.
A couple of questions:
1. Which browser are you using to view WebHelp?
2. If Pro is liike non-pro, the third dialog gives you navigation page format options of DHTML > Java Applet > Pure HTML, etc. Which are you using?
3. Is your TOC organized by books and topics? How long is the list of topics within a book? Do you have books within books?
2. Pro isn't like non-pro. i.e. you have no options like that
3. Yes there are books within books, many many topics and many books (it's in the thousands)
I have noticed that in my settings I have W3C Compliant Topics checked. I might uncheck that and see if it helps.