I had 3/6 cubes that were on the server and were not showing up in Excel. On further investigation, those 3 cubes had no "facts" associated with them. (I verified by browsing the cubes from within SSAS.) I'm surmising that Excel will display only those cubes with data in them.
In my situation, the cubes were part of a vendor supplied solution. My client did not "purchase" these three cubes, so it is possible that they contained some sort of "flag" that prevented them from showing up in the list. This probably doesn't apply to you, but it's something to keep in mind.