Which version of Robohelp are you using? While I don't remember any specific bug fixes for search results, making sure you are on the most recent patch is a good idea.
Is this only when you publish to a server or also when you run the local generated copy?
If it is also a problem in the local copy, then I think we need more information. For example, is it showing topics you have replaced with new topics? Is it showing old content in the topics that are returned in the results? Can you reproduce the error using one of the sample projects?