I'm not sure if you already knew this, or if I already made it clear - so I appologize if that's the case, BUT only one program can have a "hold" of the serial connection at a time. So, if you are viewing that output from Hyperterminal and still have that program open, no other program will be able to use the serial connection. The same goes for the Logo editor or anything else. Once any program is using that serial port - no other program will be able to "share" it. Also, I've noticed that Jemplode takes longer to find the RioCar than emplode (so sometimes it looks like the connection is going to fail but it doesn't). Finally, there were a few times that I had to restart Jemplode to get it to find my player (esp. after changing any of the connection options).

Out of curiousity, why are you using serial? I only use it when using Tony's Logo editor or when sending escher.raw and logo.raw files (and applying player upgrades).