Very nice! Sounds like you have the dreaded "out of round" (don't jump on me guys!) problem. You'll probably see this near the center section of the bottom barrel too. It's can be due to a variety of factors, including having the tailstock set too firm, the mandrel being bent, the blanks not being square to the tubes, the head/tailstock not being in alighnment, the bushings not being square on the ends, and a whole lot of other factors. Some of these can be easily fixed, and others are more difficult. If, like me, you're lazy and don't want to try to fix them all (though there are obvious advantages to fixing the problem that I am not trying to minimize or trivialize), simply do the following:
1) Loosten the knurled nut when you're done rough-turning to a cylindrical shape - if the nut is too tight, the mandrel will bow because of the forces exerted on it and/or the bushings/blanks.
2) Turn the pen to the basic shape, close to the bushings. Loosten the nut again, and turn the blanks 1/4 turn on the bushings (i.e., keep everything in the same orientation except the blank). Hand-tighten the nut, and touch up the shape. Repeat 3 more times.
This should get you pretty close. If you're really anal, repeat #2 a few times during your sanding stages, too.