Wiimote Unresponsive but Connected Classic Controller Works

I am using the latest RetroPie. I have configured two WiiMotes with connected classic controllers. They work as expected when navigating the primary retropie menus and when using jstest from the command line. However, when an emulator is launched the WiiMote start, select and dpad stop working (I think A, B still works). The classic controls all work as expected.

For snes I’d like to use the classic controllers. For nes, I’d like to use the wiimote only. How can I get the nes emulator to not turn off the wiimote buttons?