So, I just figured something out that may help other people. In RoboHelp 2015, in addition to importing map files in the Output Setup (in the Output tab, Open section), you have to select the map files that you imported when you Generate the help (I'm generating WebHelp). When you click on the Output that you want, on the left, expand the Content Categories, click on the Content <Default> (or other Content). On the right will be a Map Files: section. Select the map files that you want to include. Seems redundant, but I guess that you can have multiple Contents and have different map files for each Content.