When you print your tests- is the material rolled up tight in the back? If it's loose, it will print great untill it's tight, then you'll have overlaps.
And- someone higher up was mentioning banner material sticking to itself. Have you checked on that?
The JV3 has a weight limit on the roll. If the roll is too heavy, the machine will not be able to consistently pull the right amount off of it. Remember that the machine actually has to "accelerate" the roll every time it makes a pass, so the heavier it is, the less it will pull.
I got a new roll, it was twice as heavy as allowed, so I put it on a rack and rolled half of it over to an empty roll, and- damned material was sticking bigtime- it only took me about 5 minutes to roll it over, and it printed great afterwards.
The rack has room for 6 rolls, one over the other, put the big roll high up, and roll down, by hand, as long as the empty roll is the correct length, it's easy to keep it straight, with one hand on each end.
And- you mention feed comp around 0, heavy banner should be 80+, at least on ours, with vinyl around 20 and roll-ups around 0 or less.
As for the remote calibration, remember to put it back to 0 before starting in local, so you know which value works.