Minecraft badly controllable by external tools

Whenever I try to control Minecraft with an external tool instead of the mouse, like Chrome Remote Desktop (remote access) or TinyTask (macros for mouse and keyboard), Minecraft behaves weirdly. Sometimes when I move the cursor sideways, the FOV turns completely up or down and spins around multiple times. Other movements also seem pretty random. Aiming at sometimes with one of these programs is almost impossible.