On the center drill, if you use one, and I understand why, they are short, rigid, and common in the shop, so only use it to SPOT, then it is a 118 degree spotter, all is good, don't drill deeper than the drill point, and surely don't drill deep enough to actually start to get a center. I elarned how bad this is for the following drill in harder materials, the tips of the flutes start cutting first and get chipped, it cannot be good for the drill in softer material either is my thinking.
Do yourself a favor, spoil yourself and buy an interrapid incicator, I bought a .0005 and aquired a .0001 over 20 years ago, the .005 has been repaired once, otherwise they have served me faithfully ever since, their only downside most of us machinests never see is they are effected by strong magnets, so guys that only grind don't use them...turning on a 6" permag chuck will damp .0003 tir out of an interrapid...didnt belive it until I was shown it by a man with far more experience ID grinding than me.
Other than that hands down they are the nicest deal going, a guy turned me onto them back in 1984, so I guess it has been 22 years...I was 19 then hehe, 41 now, still on that same indicator.
It comes to mind your mill may have some "lost motion" somewhere, so with a good indicator you can dial in, and come back to 0 on the DRO from differant directions and see what ends up happening. Also I have never seen this, BUT your quill travel may not be square to the spindle bearings, I cannot imagine how that could happen on a good machine, but you can check for it.
Bill