Steve most errors can be found in the setup.
How deep are you drilling as well ?
1. Recheck your setup with a test indicator while your material is being held to ensure your rod is being held in alignment of your Z axis.
2. Ensure your drill surface is prepped with a flat surface and use a center drill to start.
3. Drill undersized leaving about .015 on the diameter.
4. Bore or use a Boring endmill with a G85 (bore in and out) to finish the hole to size this will take out any wandering of the drill or reamer for that fact.
5. when you rotate 90 degrees check with your indicator to ensure your table has located properly. (I have been amazed on how many tables are warn and do not locate properly).
Never assume that a chuck or another holding device is right on the money, use that indicator so you know, once you verify then you're off and running.
Hopefully this will help.
not met to offend anyone but to ensure understanding I post the following.
(a reamer will only follow the hold that is made for it)
(boring endmill is ground so that only a small portion on one flute will be cutting)
(G85 can be used with a L2 or L3 (repeat) command for tight tolerance holes for repeatability)
My Response to "It's Close Enough", "Is Your Tool Box and The Door Close Enough?"