First things first...

Are you using the latest version of Logo Editor? There were some bugs fixed in a recent release.

Next thing, do an ".upgrade" of the software onto the player using the standard upgrade procedure. You'll have to pull the power from the player, and don't apply power to the player until the upgrade software prompts you to do so.

If the upgrade does not work, then the problem lies in your serial connection somewhere. Bad or loose cable, for example. Or maybe something in the PC's software or hardware that's screwing up the serial port.

If the upgrade works, then mess with commands in hyperterminal and see if those work. Note that just seeing the screen in hyperterminal is not enough, you need to also be able to send commands to the player and have those work too.

If the upgrade works and hypterterminal works bidirectionally, I don't see why the flash programmer shouldn't work.