How are you moving from the Lat line to the Lon line? I think you might inadvertently be cancelling your data entry. Use the trackball to advance the blinking cursor from one line to the next and then push the "save" soft key. That works for me.
If you have a lot to do, you might want to consider doing it on a PC and then uploading. There are variety of free and cheap software programs that can manage the process. My favorite is called "GPS Utility" and can be downloaded from here:
http://www.gpsu.co.uk/
It is easy to fabricate a cable with a D serial connector if you already have a Furuno interface cable for Port 4, or you can buy one from Furuno ready-made.
If you do use the PC, always make sure that you download from the NavNet first, then modify the file with any changes or additions. A new upload erases all the waypoints and routes and replaces them.