If the player is scrolling with his mousewheel to pick a different slot in the inventory bar, only every second slot will be selected. This is not caused by a special Mouse or Setting. Wayland/XWayland changed the way how the Display Server communicates with the input devices.
Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w42a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.