If Emplode worked via ethernet before, but doesn't work now, there is a chance that the Windows Firewall is getting in the way. See if this fixes it.

Other possible problems include a mismatch between the player firmware version and the Emplode version. As you have surmised, you need to solve that serial port issue if you want to upgrade the player firmware. However, you don't need to do that simply to find out if the two versions match. Just hit the "About" screen on both the player and on the PC's Emplode software. If they both say 2.something, then that's not the problem. In fact, if your player is running 2.00 beta 13, it's already running a good version and you don't need to do anything else.