When using the feature ISP -> Start Bootloader... with FlashMagic 5.36.1792, option Baud Rate has no effect on the command being sent. The baud rate actually used is that of the programming function in the main window. You can check it with a serial port monitor (i.e. PortMon (http://technet.microsoft.com/en-us/sysinternals/bb896644.aspx)).
Fixed in version 5.37, which will be available later today. Thanks for letting us know.
Andy