When Project Designer works out which supply pins to use it chooses the ones that are physically closest to the I/O pins you are using. So it has probably selected power pins from the ISP plug for that very reason. You can, of course, choose to use any other similar pins. Alternatively you may be able to tell Project Designer to use other pins for the main I/O that are located further away and it will then choose nearby supplies that may not include the programmer.