Which device are you using? I guess it is the 89V51RD2? If so you need to Email me your schematic diagram, because your other posting makes me think you might have a problem with it.
The Start Bootrom feature is used when you implement your own ISP entry method. For example, if your code has a command line interface you might allow it to accept the command "BOOT" followed by a carriage return to enter ISP mode. By using the Start Bootrom option in Flash Magic, you can send the "BOOT" command or anything else at a baud rate seperate from the ISP baudrate. The Flash Magic manual describes some additional commands you can enter to turn on and off echo, insert delays, etc. So infact you could enter a sequence of commands, a password, etc. with the necessary delays between the commands.