That seems odd - haven't run on 3.3V power alone like that - when I cut trace it was with 5V on VIN.
Just wondering if the Serial line is commented in code?
Code:
int led = 13;
void setup() {
// Serial.begin(9600); // this line is a call and return with no action.
delay (1000UL);
// while (!Serial && (millis () <= 3000UL))
;
pinMode(led, OUTPUT);
}
void loop() {
digitalWrite(led, HIGH);
delay(1000);
digitalWrite(led, LOW);
delay(1000);
}
Also - just FYI - with USB Serial active on computer the connection is usually done in <500ms with SerMon ready to connect - sometimes a bit longer ~700ms
If that doesn't work perhaps the 3.3V applied isn't arriving properly to start as expected.