I had problems with this as well. Waxing, sanding the ends, washign down with acetnone... nothing seemed to help.
I think I finally hit on what was causing the problem. If you put enough CA glue on your pen body to be able to sand and polish it to a high gloss, it also gets that much on the bushings. If the mandrel has any wobble whatsoever then it means that the CA is flexing as it turns...
I believe this flexing between the bushing and pen body is what destroys the bond at the ends of the body. I would be willing to bet there are very few lathes whose headstock and tailstock line up exactly, which means no amount of special tweaking of the mandrel will fix the problem.
Ever since I started turning between centers, I haven't had the problem one single time.
CarveWright Model C
Stratos Lathe
Jet 1014
Half-a-Brain