I have sometimes run into a problem... I don't know exactly why this happens, and I do not know if it applies to your particular situation or not. But...
Sometimes if I plug in the serial cable after the player has booted up, or if I launch Hyperterminal after the player has booted up, I get problems. The problems are either garbage characters instead of actual serial data, or, I can read the serial port ouput just fine yet cannot send commands to the player.
If these things happen, the only solution for me is to cycle the power with the serial cable plugged in and hyperterminal already running.
I don't know why this happens so I don't know if it's applicable to what you're doing, but I just wanted to relate my experience with that sort of thing in case it was related.