Actually, it can be done using Windows Shell. The file invis.vbs in our Windows version launches the Convert program to convert from bmp format to png (and it corrects for a MuPad error in the process). At one point during development I did have the windows hidden during the compilation process, but the probability of something going wrong and being invisible, though small, would be very annoying.

A  possibility for the future is to make showing the windows optional, set by a preference. We can do this if there is sufficient demand.