first off on vp an sp models before you even get to a "fix" you need to discharge the capacitors. turn off on the front, switch off the back, unplug, press the front button four times slowly. this model line has electrostatic issues and can not be properly diagnosed without doing this first. if that doesn't make the issue go away (10% chance it fixes it), then you definitely have some kind of deep seated electrical issue. if it is just one color then you can isolate with data cable swaps (the data ribbons going into your head. do not just "wing" this ask a roland owner how to arrange the ribbons in the test).
if the issue does not "follow" a ribbon, or is across all heads then you should be considering more drastic measures. an encoder strip sets the position of the firing to the head. but that position is unilateral across the x of the head. i've heard that cleaning it will "fix" it but those times days later "it reappeared". thus not a fix? i'd start with the easy causes...
electrostatic build up on the main board
bad bath of inks
clogged/deflected heads
then move to
data swap
sometimes can be caused by a fractured main board data ribbon
all else fails
then to pulling the board and having macmedia test it, and possibly repair it
i'm about to pull my board and send it off (jv3) because i've had this same issue across all heads and it occurs at high res, disappears at 360x360. i figure it has to do with the voltage for fine dot firing (maybe carriage board, maybe main board, but encoder is perfect, and new head did not fix)