Hi Peter,
I'd like to be able to offer a comprehensive answer here, but without actually being able to audit the client's unique situation, we can only make guesses. What I can tell you is that, these days, Google is typically able to handle multiple businesses at the same address, provided the business is clearly unique, has a unique phone number, a unique landing page on the website and other factors like that. Here's a post on Search Engine Land about multi-location SEO problems: http://searchengineland.com/local-seo-multi-location-businesses-224732
Being very general here, your third location is likely not showing up for a branded search because:
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There is a problem with the listing, like a shared phone number, a violation or NAP confusion.
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The location isn't 'strong' enough in some way to be shown for the search.
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Something odd has happened, like a merge.
My best advice here is that you get the client's permission to share their story over at the Google and Your Business Help forum, sharing complete details in hopes of getting a TC to take a look with you. But, I would only suggest you do this after you have ruled out some/all of the above so that you can tell the TCs your listing should be clean, strong and guideline-compliant.
Hope this helps.