I used to run my EQ6 via sky safari with no problems.
I have a keyspan RS-232 > usb device which plugs into the base of the Synscan hand controller. Assuming you have the port & driver selected correctly it works without problems.
I still use this on my TAK NJP, but plugged directly to the Temma unit, not thru the hand controller, as there is no available socket on a Tak HC.