First check that it works OK with one of the sample projects. Click Open on the RoboHelp Starter page and then click Samples in the ribbon on the left.
If it is OK there, I think my next step would be to generate all the projects again, making sure that they all have the new layout.
What is your search panel sitting over? If you search on opening the merge it would normally still be showing the search input, then Index, Glossary and Favorites with the books below. I am wondering if you have been customising the layout and if that could be affecting things?
See www.grainge.org for free RoboHelp and Authoring information.

@petergrainge
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