It's probably due to UAC. I haven't tested it myself. However, if you're saying that notepad opens up, and notepad is an exe itself, then I see no reason why other exe's wouldn't open other than UAC stopping you. Obviously letting batch files run exe's on your pc without your approval wouldn't be very secured.
Also, doesn't flashing the bios from a floppy need to be done at bootup and not from windows? Why do you have to automate a bios upgrade? It only takes about 5 minutes. I don't see how answering "yes" to the question if you want to upgrade your bios is so tedious as to need to automate it. Automation is for system builders that have hundreds of boards to upgrade and even then the board makers usually have a utility to help them with automation.
