General rule that I always try to follow: "If I'm not happy with something, tell the person who can do something about it." In your case that means talking with the LBS owner about it. From what you describe, I would want to keep the relationship a positive one. So, if he is responsive, I'd tell him how much I appreciated it and bring in some donuts, six pack of beer (or something that I know or suspect will be appreciated) to say "thanks again."
In terms of are you being anal? In the minds of many you probably are. But so what? I'm not so sure that being anal is a bad thing in all situations. I know that I absolutely hate doing any repair work on guitars for others or myself that isn't as close to perfect as I can get it. Everytime I see the instrument the first thing that grabs my attention is the flaw I wasn't able to repair. Hence, what should be a nice experience, looking at wood instruments, is lessened by the flaw. If you feel the same way about your bike, that is it has aesthetic value to you, then you're being smart to try and resolve it.
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A conclusion is the place where you got tired of thinking. - S. Wright
Favorite rides in the stable: Indy Fab CJ Ti - Colnago MXL - S-Works Roubaix - Habanero Team Issue - Jamis Eclipse carbon/831