... the cap is drilled and threaded and then I take a final cut to size with work supported with a revolving center - I tested the revolving center to a point turned in the chuck - looks lined up fine.
I can think of a couple of ways this might cause the end of the cap to deflect a little (and a little is all it takes, no need to ask me how I know this!)
I cut away the first 2 or 3 threads from inside the cap (it creates relief for the partially-cut threads on the barrel as it screws tight). If you don't do this, or if the ithe end of the cap might deflect as you tighten it up. (That might still happen if your live center isn't perfectly aligned, or if it has some crud on one side where the cap end sits.)
Same thing with the barrel -- which is typically drilled and tapped to receive the nib section. That can deflect as you tighten the live center into it.
I've had a lot less trouble with this since I started using custom-made pin chucks to hold the barrel and the cap for final outside shaping. (Rick Herrell made them -- check in the vendor area here.)
1 is it the drill ?
2 is it the die sitting not flat in the diestock holder ?
3 barrel collar not in line - this is turned with the revolving center - so this should not be the problem ?
4 revolving center - not turning true ?
I suppose all of these are possibilities, you can test for some of them -- such as the live center not running true (put something hard in a tool holder and gently move it against the 60 degree cone while the workpiece is tight against it -- if you hear the tool tapping on the center, you have a problem, if it scrapes all round you are in excellent alignment.)