The gamepad support leaves a lot to be desired; I know GTA3 had the axises backwards on my PS2 controller, while SA wouldn't let you bind the D-pad so you couldn't mimic the PS2 control scheme on it. Luckily with SA there's a program called SAAC that'll let you fix its control issues, but you need to downgrade to v1.0.
Does your mouse work outside of the game? Do you have or have you had a controller plugged in? Check the game settings to see if the input is for your mouse or something else. Try unplugging and replugging your mouse in.
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