Yes very annoying. This must have something to do with the
previous bug with the throtlle and rudder not working when mouse was over an open toolbar window. That was fixed in SU8 beta but this new behavior was introduced. I use a third party program Voice Attack to speak the commands. When the mouse is over a panel window the program is not listening.
This is seemingly still not fixed even on SU10 beta.
I have this issue even when hovering the mouse over a GPS screen. I just took a flight in the Just Flight Hawk and when I had left my mouse pointer over the GPS screen in the centre console (where the hud should be) I couldn’t use the joystick buttons I have assigned to ATC selection 1,2,3, etc.
Didn’t try on the keyboard (I’m in VR ) but I imagine it’s the same.