Matt,
Thanks for your post!
Usually the reason that a shapefile does not display in Map Suite Explorer is due to the MapUnit not matching the coordinate system of the shapefile. One of the properties of the Map is the MapUnit where you can set it to DecimalDegrees, inches, feet, yards, centimeters, miles, meters, and kilometers. Depending on the Projection of your shapefile it could be any of the above, although most are in Geodetic and use the Decimal Degrees setting.
It is somewhat difficult to diagnose problems such as these without having the problem shapefile at hand. If possible you might upload it to our Customer Portal (helpdesk.thinkgeo.com), if under 3MB, or our FTP server if the file is larger so that we might review it.
ThinkGeo Support