thx for the design.
You are talking about this part? (see attached)
This looks like inverting both signals. Maybe, that will help. Will test it this evening on a breadboard.
Edit: No, only inverting, if DTR and RTS are different level. And high-level in all other cases. Sounds logical.
And: RTS is feeding GPIO0; DTR is feeding RESET. Thats vice versa to my actual signal flow.
ESP8266 Arduino add-on
Arduino IDE 1.6.5