paindoc, I feel your pain. (oh, ho ho, I just had to get that out!)
Well, I went and looked at mine and sure enough, my cupholder door is slightly misaligned, too.
The only thing I can tell you is that it took me about 9 months to realize that...and only when you brought it up. My glove box door is also slightly misaligned, but I didn't figure that out until someone mentioned it on this forum.
Bottom line is, if anything like this is like a burr under your saddle (I am from Texas so I have to use Western metaphors) you may want to do something about it.
But fair warning, the cure may be worse than the disease (oh, ho ho, I got another medical metaphor in this post). Several posts from people who tried to get their glovebox realigned made me think twice about trying it.
I chose to leave "well" enough (another medical metaphor...man, I got a million of 'em today) alone.
