I can’t speak for the original poster, but I found the command line to be the only way to get GPIO to work in OH V2.0, I can’t speak for V2.1 as I have enough work trying to get my RFXCOM device to come up in a predictable fashion.
After the unreliability of GPIO for inputs in OH V1.9 I’ve transitioned all inputs and most outputs via MQTT to ESP8266 Devices (Adafruit Huzzah) running ESPEasy. At around $10 USD a pop it is much better use of my time than continually battling GPIO problems. The ESP’s have been very reliable as long as I reboot them once a month which I do with a script that looks at their uptime
details my journey
I set the initial state of GPIO Pins via a Linux Script ran from Crontab which gets around the original problem of all inputs turning on when OH starts