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Unfortunatley we have not experienced such problems to give you a comprehensive answer - but I do see sites drift in and out of the related web pages listings; this is probably the case with your directory, does it show up for other businesses and just not show for that client's site?
It could be that a piece of data that Google is matching on has changed; is the adrress and business name still 100% correct in Google? There's every chance that the poor matching that has crept into some things recently has started to cause another issue (like Google associating odd addresses to web pages and wrong pictures to other non-local listings).
How has the traffic held up for the directory? Are all of the pages still indexed?
The more info you can share with us the more chance there is of finding the problem (without getting too specific - we don't want to know which sites or which company).