I had another look on it tonight. So far I am only trying touch an go landings with the 787. That’s why I start all of my flights with running engines on the runway. Tonight following worked for me for different airports. Before takeoff I open the extra menu and click on one of the items. Afterwards the USB controllers freeze. Fortunately my mouse still works. Then I am pushing the levers forth and back multiple times. After a few seconds the USB controllers work again. And most important they work during the complete time - I am able to use the ATC during the flight as well.
Maybe this also works for you when you use your keyboard and control the levers with it?