[GrizHFMinimill] Strange mill problem

I have an X2 HF mini mill, R8, with the stock bearings and a belt drive. I'm having problems with something causing tool runout. If I measure inside the spindle I get less than .001 runout (~.0007). If I mount a collet and a tool in the spindle and tighten down the drawbar and measure runout on the tool surface it is .007 or .008. This happens with all my collets and mills and drill chucks and bits, so it is something to do with the mill spindle. It's as if the collets are askew in the spindle, not parallel to the axis of the spindle.

Can anyone shed some light on possible causes? I saw a post somewhere that said if the key in the spindle that goes in the slot in the R8 collet is too tall it can cause problems. Has anyone seen this happen?

Help or advice will be greatly appreciated!

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