The linearity of each of the 12 oscillators is adjustable. However the autotune is responsible for tuning each oscillator up or down overall. So the question is what kind of tuning problem do you have? If you just notice VCO-1 and VCO-2 are out of tune with respect to each other, it's a linearity problem. The amount of beating will vary depending on the oscillators' pitch. Some voices VCOs will be more in tune than others.
If some voices are drastically out of tune with respect to other voices you may have another problem. For example two voices maybe more than a semitone flat with respect to the other voices. Judging by your post it sounds like this is the kind of problem you're having. If this is the case, calibrating probably won't fix it. This happened to me and it went away after adjusting the connectors and turning it back on. There's a post on this board where somebody had that kind of problem go away after installing Europa.
You can adjust it yourself if it's just a linearity problem but it may be more involved than you're expecting since it's 12 adjustments and there's no absolute correct linearity. The linearity procedure in the service manual gets the oscillators as close to the ideal as possible for a range of pitches by looking at a test point output on an oscilloscope. So I'd recommend following that procedure, although you could get away doing it by ear and matching VCO-1 and VCO-2 for all voices. You may as well do it right if you're going to open it up and adjust things. You could do the calibration procedure with a multimeter, sound card oscilloscope software, and some probes connecting the Jupiter to your sound card audio input.
If you want to experiment before you open it up you can do the following to see which voice is doing what:
Split the keyboard 4-2. Put both sides on "Poly 2" voice assignment. Hold a note and then play and hold another. Do this for any four notes on the four lower voices and any two notes on the upper two voices. Poly 2 assigns the voices in order on the 4 voice board (lower) and 2 voice board (upper). You can figure out which voices are acting strange and test them at a variety of pitches to get a feel for what the problem is.
