If you use Flexi, in the "Contour"-Tab of the "Rip & Print"-Window you have an option "Rotate cut job". This will let the RIP rotate the contour cut markers horizontally. A customer of mine is using that for contour cutting with his 64" Latex an Summa S75.
Interesting side effect: if you use a summa, increasing the number of markers will lead to more contour cutting accuracy.
This is the link to a video I have created for my former company, how to increase cutting accuracy with the commonly shlightly deformed latex print jobs. You will find the procedure to print the markers rotated from 1:08 (the video is in english).