If you are using EQMOD, have you set your site coordinates within EQMOD? If they are in the wrong hemisphere the scope will be running west to east not east to west.
If that is happening it also would mean if you manually slew the mount back to where Jupiter is for instance, the scope is pointing where it thinks is on the wrong side of the meridian the sync will fail. EQMOD won't accept a sync that is on the opposite side of the meridian to where it thinks the scope is pointed.
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