Alex
Peters post is spot on. There is no N/S switch in the Gemini its on the 492DD controller. N/S is set by the local lat/long/DTG/timezone you input. Remember "-ve" for latitude.
See
here for entering DTG Gemini style. (link at bottom of page. DTG format is for G1, the G2 is input differently). You already know this but its always good to check these. Also check local Lat/long/timezone as these can conflict throw off planetarium programs.
Also check you have Ra on Ra axes and visa versa DEC....an oldie but goodie. Bad battery in the Gemini2 and 1 can cause loss or corruption of data so check battery
Stallerium is a pretty stable program id expect it to be correctly using the Gemini settings but do check