I had the exact same problem and researched it on the forum. There are a lot of good tips, but one struck me as kind of crazy. They said make sure not to tighten the knurled brass nut on the end of the mandrel too hard, as that could cause problems.
I checked headstock and tailstock alignment - good.
I checked for mandrel bend - 0.002". Straightened to 0.001".
I checked that my live center was truly 60deg - nope. Bought a 60 deg center.
So, I go off on my merry way and turn another pen just as completely out of concentric as the previous ones. Hmm.
The only thing I didn't deal with was the brass nut tightness. So:
I assembled another pen on the mandrel, measured the runout at the center bushing with the nut barely tightened. 0.002". I tightened the nut snug, but not crazy tight. 0.005". I tightened it white knuckle tight. 0.015". Yikes - the nutty guy (just kidding) who said don't over tighten the nut was right. But why???
I proceeded to check a number of things and to make a long story slightly less long, it was the squareness of the end on my blanks. I had been hand aligning the blank on the drill press using a pen mill to cut the ends, figuring it was accurate enough. It wasn't. I rigged up some V-blocks to hold the pen blank securely and drilled with the pen mill and got much better results. Now I can tighten the brass nut down like crazy and get 0.002-0.004" runout at the bushing max. My pens now don't turn off center.
I think the key issue here is that everyone does things a little different. If you have a dial indicator and magnetic base, you can duplicate my experiment easily and determine if that's your issue. If so, the simple solution is to improve the squareness of the end cuts on your blank. Using a pen mill with the guide reamer and holding carelessly was not satisfactory for me.
Good luck. I'm sure you'll solve it.
Sandy.