Great that it works now.
Especially for large Flash memories, there is a High Speed option in FlashMagic.
Options/Advanced/select Checkbox 'High Speed Communications' and '12 clk'
Now it connects first with the slow baudrate (9600), that you've selected,
and then it switches to the highest possible baudrate (without any measurements)
for programming the part.
I've never tried this option, but maybe it gives you a faster programming time.
Cheers,
Christian