Most common problem when using Hand Controller and computer at the same time is issuing a bad sync. For example, if you slew to a star or object with SGP and sync with Hand Controller, it’s a HUGE BIG NO-NO-NO. Never ever sync on a star or object with a different device that was slewed with another device.
In other words, if you slew to an object with Hand Controller, sync with a Hand Controller. Likewise, if you slew to an object with computer using planetarium software or equivalent (i.e. SGPro), sync with the SAME software that you slewed in the first place. Never ever mix Hand Controller and software for slewing and syncing otherwise the scope will be pointing to very wrong position (i.e. pointing to the ground).