Sorry the quality is so bad. Hopefully you can see the signal blanking out as I switch between the menu and the running system. The monitor's HDMI2 input notification appears in the top-right each time this happens.
The output resolution is 1080p@60 in both the system and the menu (I tried to show this but it's hard to see the monitor's OSD).
It feels more like the SDL window(?) is being recreated as I switch between the system and the menu.
With the FKMS driver, the monitor never blanks out and switching between the running system and the menu is instant.
When you map keys with "m" on the virtual keyboard, they get stored with the "keymap", not hotkeys or joystick map. You have to "save current keymap to" to save it to a file. Then you have to change the "Active Keymap" to "Positional (user)".
I actually did another step by manually loading the keymap before I quit vice, but I don't think you need to do that. The next time you load up vice, the user keymap you saved should be loaded.
@RedNifre It depends on how it's compiled on Ubuntu. On Retropie, it uses SDL2 for the UI (as Emulationstation), on Ubuntu I assume it uses GTK3.
If you want to dig more and submit a bug report to the Vice project, you can try enabling only the SDL2 UI when compiling Vice and see if you can reproduce the problem also on Ubuntu.