I'm a very big fan of custom missions and I've, in the past, downloaded them from Pharaoh Heaven's website. When I had the game installed on my PC using the CD they worked( showed up) in the custom mission list. However, in this version they don't show up on that list at all. Is there a way that I can get this version to recognize those maps? Any help or advice is much appreciated.

Just place the maps in the usual location (<install location>/Pharaoh/Maps), ensuring that the required .map file has been extracted. It should show up normally in the Custom Missions list.

If it isn't appearing there, then it might be that you have UAC enabled (user account control), which is placing the files into the VirtualStore, where the game cannot read it: In this case, you should disable UAC and restart your PC, then try to add the map files again.