Go into the Setting for the job. Look at the Media settings. Size should be Custom ROLL. In that way, it should take the full size that is being passed from your design package. Also, just check the Width and Height settings just below the Size.
I print directly from Illustrator, however Illustrator will not use and Artboard of 6 meters, normally about 5, so what I do is size my job to half size, 3 meters x 0.6 meters. Then in VersaWorks I scale it to 200% and then print it. I often print 6 meter x 1.2 meter banners no problem.
Neil