Frank
If I understand you correctly, you are using the Microbit USB port Com1 to make connection with your K3, and you are trying to use the DTR/RTS on that Com line to key your radio. You have set the K3 and N1MM+ both for RTS/DTR keying. If my memory serves me correct, unfortunately, that setup doesn't work- the Microbit USB ports won't pass the DTR/RTS signal for cw keying.
I'd suggest that you use the RRC internal Winkeyer. I have mine connected here, and it works quite well. Only downside is that you must go into the RRC setup if you want to operate RTTY instead of CW. If you want or need more info, let me know and I can send it along.
Dennis W1UE