Definitely change your print direction in your RIP. That would be the easiest way. Alternatively, although I'm not sure about the JV3, but on the JV33, you can change the priority of the Print Mode from "All Panel," "All Host," or "Individually."
Choose FUNCTION > SETUP > PRIORITY
All Panel = All settings controlled by the printer's front panel
All Host = All settings controlled by the RIP
Individually = All settings controlled on an itemized basis (MEDIA COMP. / HEATER / PRINT MODE / INK LAYERS / DRYING TIME / AUTO CUT / PRE-FEED / MARGIN / COLOR PATTERN / REFRESH / VACUUM / FeedSPEED LEVEL). You can choose whether each setting is controlled by the printer's front panel or the RIP.