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I've activated the Auto-synchronize TOC checkbox like you said. This works. However, it only works in some of my projects. In the other projects, it doesn't work. This has me stumped because it works just fine in some of the projects.
I've been doing some experimenting with the options in that Windows Properties dialog box found under Edit-Windows.
I created a brand new test project, which contains only one topic. I added that one topic to the TOC. Then, I performed 2 tests as follows:
Test 1: I selected Windows from the Edit menu to open the Windows Properties dialog box. I looked at the Search checkbox to make sure it was checked on. I generated my primary layout. In the Microsoft HTML Help window, there was, indeed, a Search tab.
Test 2: I re-opened the Windows Properties dialog box and removed the checkmark from the Search box. I generated my primary layout again. However, the Search tab still appeared in the Microsoft HTML Help window, even though I unchecked the box.
Test 3: I changed the content of one page of my project. Then, I re-generated my primary layout again. This time, the Search tab disappeared from the Microsoft HTML Help window.
In summary, it appears that the options in the Windows Properties dialog box do not affect the primary layout unless some content in the project is changed.