The water should be on the same side as in Azgaar's generator (but not the roads - they are not synchronized). If it's not then it's a bug, I'll check it. Meanwhile you can rotate the map in the "warp mode": click "warp" and then shift+drag to do it. If needed you can reset the compass rose (ctrl+click it) without affecting the map itself.
Viewing post in rotate layout/compass
It is a very great option, but maybe it is not intuitive enough. A text "shift to roteate the map" on the screen can help. Even "ctrl+click to reset the North" text can appear on the custor when it goes over the compass.
I take this opportunity to congratulate the developer of this wonderful software