Which version of the IDE are you using? I tried to replicate you situation, and I managed to do it, but this is what I did:
1. Opened my Arduino IDE.
2. Selected the correct COM port.
3. Selected the wrong board (I selected a Gen1 but I used a Gen2)
This made the IDE show the "transfer complete" message but also caused that the sketch never started, did you set the IDE configuration for your board correctly?