If your program is using the RS232 itself, you can find that there can be stuff left in the Windows receive buffers.

You start Flash Magic, and FM fetches this old stuff from Windows rather than the bootloader communication.

You can solve this by judicious use of the startup time parameters.
This is from a generic makefile. I use long times for "make erase" which means that I can manually hold the 8051 in reset before FM gets started.
The regular "make program" will work normally. i.e. the DTR line is toggled by FM.

######################################################################
#
# if the existing prog is echoing RS232, then power up <5 sec of erase
#
# probably as easy to use FlashMagic application with its terminal.
#
######################################################################

erase:
	fm.exe DEVICE(P89C51RD2Hxx, 18.432) COM(1, 4800) 
		HARDWARE(BOOTEXEC, 5000, 100) 
		READSIGNATURE READSTATUSBYTE 
		ERASE(DEVICE, PROTECTISP)

program: 8051.hex
	fm.exe DEVICE(P89C51RD2Hxx, 18.432) COM(1, 38400) 
		HARDWARE(BOOTEXEC, 500, 100) 
		READSIGNATURE READSTATUSBYTE 
		ERASE(DEVICE, PROTECTISP) 
		HEXFILE(8051.hex, NOCHECKSUMS, NOFILL, PROTECTISP) 

 

You can probably use the FM GUI but life is difficult with GUIs.

David.