I don't have that problem? Have you set joystick keys to dpad in the settings?
Input Mode - Joystick, Key Press fix on
Buttons - Hide Buttons
Settings - Frameskip=0,Smooth Resize, Resize Mode=Full screen, Joystick Keys= dpad
Keyboard set to game keyboard. In the game keyboard settings I have a default profile where l1,l2,lr1 and r2 are set to f1,f3,f5,f7 a c and d are set to space return and joystick up. I then have extra profiles for games that use different keys (eg I have one for skool daze). Remember to have an extra default profile where hard key mapping is off for wheb not using anvice.
Finally when showing buttons on anvice with joystick selected for the input pressing 2 will take you to the vice menu.
Here I use
Video Settings - Video Cache off
Sound Settings - Buffer size = Between 50 and 75 (see which works best for you), Fragment size = small,Frequency =44100, Syncronization = Flexible.
That gives me near perfect emulation. Sound still has latency in some games, noticably rollaround