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I bottled my second batch of beer, a nut brown ale recipe from northern brewer. I added coffee to the secondary, and my first bottle I had after 2 weeks bottle conditioning tasted like a nice coffee nut brown, though slightly under-carbonated. Now at three weeks the carbonation is good, but the flavor is inconsistent between bottles. They all conditioned together in a failry dark corner of my bedroom. the temp varied slightly, but all the bottles would have been affected by this. Every long-neck bottle I have had now (3 or 4 total) have tasted great! My shorter bottles (Anchor and Sierra Nevada pale ale bottles) though are really inconsistent. one has been good, but the other two I've tried have had very little coffee or nut flavor and a metallic, chemical-like taste to them. Anyone have any ideas what could be causing these inconsistencies?

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To support Chris idea, were long-neck bottles new, never used? –  Paolo Mar 14 '13 at 10:32

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The metallic/chemical taste to me suggests contamination at the bottle level. Maybe some of these were insufficiently cleaned or sterilized. The wrong microbes could also impact the flavor by breaking down the flavors you want into ones you don't. Is there any possibility you put more care into cleaning the longer bottles (as they would be possibly more difficult to clean?

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