I'll add my reply to this old post in case anyone else comes across it while looking for information about RAppID BL program, like I did.
I've been using it with TRK-MPC5604P and have had numerous problems with it. Yes, the program works well, if you pay attention to all the nuances. 1) if you are working with CodeWarrior for MCU and running in debug mode, then cycle power to the target prior to using RApID BL; 2) if you are using the USB serial port for communication with the target, either your own or FreeMaster, exit the PC serial port program prior to using RAppID BL so that it doesn't hold the serial port; 3) if you have modified the jumper on the TRK target, so that you can grasp it without using a needle nose pliers, make sure that the connection as still making proper contact, (super glue tends to coat the contacts and those FABS jumpers are tough to manipulate); 4) if you are using some other USB device, (like a USB scope or logic analyzer), make sure it does not conflict with the RAppID BL USB driver; 5) if you have been using the REG_5V supply on the target, but have moved your location, make sure you provide a proper power supply, or switch back to the USB_5V supply.
If you can avoid all this little issues, then RAppID BL works pretty well.