By default the VCC line on the 6-pin programming header is not connected to the board VCC signal. This is to ensure that someone wishing to program the board does not accidentally drive an LED strip from a USB power source. So to program the device, it forces the user to connect the real power supply to the 2.1mm jack as well as the 6-pin serial connection.
BUT if you want to override that and ensure you don’t have LEDs connected when programming over USB-serial, then you can connect the jumper. This will connect the serial VCC line to the board.