Ken,
Did you ever try dumping the first couple ounces to see if the flavor went away or did you not even suspect the beer lines until you cleaned them and didn't test that variable?
Hi Beersk: I did not test that variable. Do you think that the beer sitting in the line absorbs a bit of whatever is "dirty" and is in worse shape than the beer that follows? It makes sense. I was actually trying to picture what was happening: Small particles of funk are stuck to the sides of the lines and it comes off when you tap a beer and you end up tasting it. But the beer in the line has had more contact with the lines and so that's the worst part. Seeing as this was one of the more pronounced instances of 'funky beer lines', my strategy going forward is to clean the lines far more often. If your question is pointing to something that I'm missing, please let me know.
Yep, that was kind of what I was getting at. The beer sitting in the line absorbs it and affects the flavor. Not an issue with regular cleaning though. I think a thorough cleaning every 3 or 6 months is probably about all you need depending on your turnover. I mean, if you cared about longevity of your beer lines, after every keg blows works, but that's just more work than I want to put in. Since I change my lines out annually, I don't worry about it too much. But then again, it really isn't that much work...and I've got all kinds of time these days.