fat 16 has a max size limit of 2 GB
you need to reformat to at least fat 32 as fat32 is much larger than this
wintoflash is for installing the os via usb is that right?
it may be best to format the drive in os first, as i believe this program is still in beta and this could be causing the problem
try right clicking on the drive in windows explorer ad pressing format then choosing the correct option and ensuring you have set the correct capacity which is the top option
you have you dont need to use any 3rd party program,
what os are you using btw?