Yeah.... to be perfectly honest I feel like Nakaya's quality control has gone down a little in the last couple of years(I mean a tiny bit). When I first bought a couple Nakaya pens back in 2008 they were absolutely flawless, I mean everything about them was basically perfect. The last few Nakaya's I've purchased (earlier this year) have had slightly sloppier urushi work. It hasn't been bad enough to want to send them back or anything, but to my eyes it's definitely a little messier looking. I'm talking about the simpler tamenuri finishes(aka,kuro,heki), nothing crazy like the maki-e, and stuff.
I already had the feeling the quality control was slipping a tiny bit, and seeing this post has kind of confirmed that for me. Now you have to keep in mind that they're so backed up with orders because of thier popularity, that this kind of thing was bound to happen sooner or later. John Mottishaw told me that the haven't really been able to get any pen pillows done, because they need to focus on the pens first and foremost. I've been asking about a pen pillow for like 9 months, and still was told it would be January at the earliest. The other thing to keep in mind is that some of the guys making these pens are probably old, and they may have had some retire recently; Who knows really. All of this could contribute to a couple of minor flaws making it out of the factory.
If I were the original poster I would just chalk this up to the "wabi sabi" nature of a truly hand made pen like the other guy stated. Thats how I look at.