So I thought I would do a little test and connect hyper terminal to gpsapp and just type "EARTHA" and see if it would respond with "EARTHA", but nothing happens.

Great test! Good idea.

Are you sure that the serial connection to the player is working? Can you "Q" to a shell prompt, for example?

What could this mean?

It means that either GPSapp isn't seeing the EARTHA (i.e., serial problems either software or hardware or cabling), or that there's a bug in GPSapp that's preventing it from responding. You sure the GPSapp binary is the most recent one?