We have a problem on our 3360, when we panel jobs, there is colour differences between each panel. Example we printed a 7 panel job on mesh solid orange, and we got different shades between panels. Vutek give no real answers
If you're talking about difference on whole height of panel, you can try in Colorburst in "tilling options" turn on "automatically rotate every other column"....
Yes, I have experienced this problem many times on our 3360. The biggest factor that I have found is that the platten is uneven, so when you gap your printhead in a specific point it is really higher and lower left to right on the platten.
There are adjustment screws on the bottom of the platten, but you need the guages which attach to the side of the carriage. I say this laughingly because Vutek says you are supposed to be within .001" and the screw is course thread. Anyhow, we have found that over time (heating and cooling) that the platten warps and therefor needs to be readjusted every year. I have a set of the gauges so fortunately I don;t have to call service out to do this.
You can remove the platten and print and see if this makes a difference. Not sure if you use unbacked mesh and run with the platten off already though.