General Options: Voltage Settings

Target Power

Even if the first thought might be: "Here I can specify the target voltage for the system" it's NOT!!!
The provided voltage to the system (Pin 19) will always be the voltage provided via the USB Bus connection - so basically 5V due to USB specification (one exception is the Flasher Portable which provides about 4.5V to the system via Pin 19).
If you need a different supply voltage for the target you have to either power the target from external, or you can use an adapter such as: Segger Target Supply Adapter
The value behind Target Power specifies the the amount of time between powering the target (using Pin 19) an the start of programming.

Fixed VTref

The Flasher will check if the target voltage (using VTref Pin (#2)) is at least above 1.1V after the time specified with 'Target Power' before the programming will start.
Also the (measured) voltage of VTref will be used to specify the IO voltage for the other used pins (identical to the measured value).
If (for whatever reason) the VTref pin is not connected to the target power this measurement will fail and neither the programming will start nor the output on the needed IO lines will happen.
In that case the Fixed VTref can be checked to prevent this measurement and to work with the specified Voltage (instead of measured) in the line below