After the app has been open for some time, reconnect the Duo and using the app to unlock fails. The App reports “Incorrect PIN entered” and the Duo flashes red.
Yes, I’m entering the pin right. 
I can unlock the OnlyKey on the Duo itself with no issues. Restarting the app fixes this issue as well.
App v5.3.6
OnlyKey DUO v3.0.1-prodp
Is it possible you press a character on device then you enter PIN in app? Say touch 1 button then entering PIN in app would result in incorrect PIN.
I actually thought that might be it, but it doesn’t seem to be. My pin is currently 9 digits long. If I had touched the device and then entered my pin in the app, it would not be wrong for every future attempt.
That said, I’m not seeing any yellow flashes when I plug the device in.
This only seems to happen after the app has been open for at least 2 days.