Ok, so when you turn the spindle 1/2 turn, its exactly the same that way too then right? (I apologize if you already said that, I just did not see it)
But yes if thats it, you would need to shim the front of the column. The one that is on 0 is towards the front of the machine right?
You'd notice it on a fly cutter, but probably not on an end mill. If your spindle is at .0015 high in the back and .0015 low in the front over 2" Each, and you have a 1/2" end mill in there, its a much much smaller difference. But it is better to get it perfect, the closer it is the easier.