Each carb has to be adjusted in relation to the idle set screw on the linkage which controls all the carbs.
Carbs 1and2, 3and4 are connected with little shim like strips which you probably know of. They are thin and work as a stabilizer for each pair, but if your adjustments are out of a certain range, they will pull or tug on the other "neighbor" carb and can alter it. Some change between pairs while you're syncing is normal, you gotta just fiddle with it.
Now, as far as adjusting one carb and other carbs in the other pair being affected, well that's probably an issue with you adjusting til one slide hits the bottom and, of course, it physically raises the entire linkage. Which goes back to the first sentence. This is where a good bench sync helps to get a lot of these values dialed in really close so you don't have to worry about staying within the range of adjustment.
Syncing without keeping in mind the idle adjust screw can also mean that it might have no affect cause where each carb is set the idle adjust screw might not even be touching.
As a guideline, here's an easy trick. If the individual carb adjust screws have 3-4 threads showing above the nut, you will be able to sync with enough range of motion in the idle adjust screw (probalby).
Knowing that, first get all the slides off the deck, so you aren't hitting the bottom. Select one carb as master, get it to that 3-4 threads showing, and then set idle adjust to whatever size drill bit you have (around 1/8").