You can't issue Sync commands via the cable that connects to the hand-controller and this is essential for performing star alignment.
Ditching the hand-controller and using EQMod can be a bit disorienting at first, but if your mount is accurately polar aligned you will
eventually reach the point where you will never want to see the hand controller again

There are numerous other benefits to
connecting to the mount this way, including the ability to do your star alignment (and polar alignment) using plate-solving via
AstroTortilla or similar package.