Clicking run is just allowing the tool to be ready to flash as soon as a suitable connection is established.
You can click it after getting into bootloader mode if you want.
Put your toothpick or other device in to press the reset button and then press the power on button to get to bootloader mode.
It can be a little hit and miss as sometimes I have to keep the reset button held for a second or two but if the timing is out then it will start into normal boot mode, at which time I just pull the plug and try again.
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