I created a .mshc help file using PackageThis. The root node "PackageThis" showed in the TOC but the children didn't. If I search for the missing pages they are definitely included.
This is been an on going problem. There can be different versions of Help modules (C++, Blend etc) installed. They have the same topic IDs. To get around this problem and make sure that the TOC looks neat and several page versions don't all get merged together, Microsoft checks each topics "Microsoft.Help.TopicVersion" meta tag.
Looks like anything can be merged into the root -1 on either VS 10 or VS 11.
PackageThis has had base node PackageThisRoot.htm, ID="PackageThisRootID" we parent all help into.
If I delete the TopicVersion tag from PackageThisRootNode, then VS 11 will show packages parented onto that node. But VS 10 wont.
The solution is to do away with the PackageThis dummy node, and parent help into the root. For PackageThis application we now change all topics version meta stamp to version=999. That way all topics downloaded will at least play properly with each other in the TOC.