Hi, yes. Simply turn off Virtual Mouse in Amiberry/Input settings before you start the emulation.
Taken from FAQ:
Virtual Mouse Driver in AmiKit enables a smooth experience when switching between Amiga and Linux apps. However, some Amiga programs (like AmiStart, DOpus and probably others) might not fully register such a mouse pointer. For instance, a DOpus' menu doesn't work correctly if invoked by the right-mouse button over an inactive window. The window under mouse the pointer has to be activated first (with left mouse button). Anyway, you can always disable Virtual Mouse Driver in Amiberry Input settings. Just bear in mind that it has to be done before the emulation is started (it cannot be enabled/disabled on the fly).