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It sounds like your parent TOC contains the TOC entries for the child projects instead of references to the child TOCs.
See the topic on my site about Merged WebHelp and see how I explain creating the TOC.
Thanks for your reply and samples, but after all I had done the merge correctly (separate TOCs in the merged projects). Here was the issue: my default browser if Firefox and it takes from 5 to 10 seconds for the TOC to refresh if one of the child projects is not installed. I was waiting only a few seconds and, not seeing the TOC content, just closed the browser thinking the TOC was broken. I opened your samples in Firefox and IE and see the same slow Firefox refresh. Bad Firefox 22.214.171.124. Have you encountered this before?
Issues with Firefox loading have been reported and are documented on my site under Browsers. There are many workarounds that various people have contributed.
Not aware of the issue being made worse by not including a child project. Haven't seen reports of that. My own merged webhelp is always delivered in full. We merge because of project size.