Arduino fast start not working properly
The reason for this issue is to do with SPI.

Basically in my custom arduino I have a 4Mbit flash and it communicates over SPI.
It seems that when the RST pin is connected it also automatically initializes the SPI protocol.

When the arduino is powered from RAW + GND directly from an external power source you need to initialize SPI manually.

In your sketch you need to:

    #include &lt;SPI.h&gt;

    void setup() {
        SPI.begin(); // this needs to be invoked before any SPI device gets initialized

        // initialize and use SPI devices
    }