That is another bug I'm going to look at soon (lots to do, haha). For now there are a couple workarounds:
Option #1 (Easier, but slower on many devices)
- ENABLE Settings->Virtual Gamepad->Redraw All
Option #2 (Also easy, but a few extra steps. Faster on many devices)
- DISABLE Settings->Virtual Gamepad->Redraw All
- DISABLE Settings->Virtual Gamepad->Display FPS
- Change Layout: Settings->Virtual Gamepad->Change Layout->Mupen64Plus-AE-Touch
(if your device has a small or tiny screen resolution, choose the Touch layout for "Small" or "Tiny")
This bug came about because I created a workaround due to the Android API for redrawing graphics being uber-slow (redrawing the frame creates a noticeable lag on many devices). Unfortunately the workaround doesn't work for every device (some devices it causes the rest of the frame to disappear, making the buttons invisible). This problem will be fixed definitively when I implement the drawing in GLES2 rather than the Android API (been focused on other things, so haven't gotten around to this yet)