I brewed several hefe-weizens this past summer (requests from friends for BBQs and parties). When I used the late addition method, the resulting brews were light-colored and excellent-tasting. Craft brew quality. In early September I brewed another batch for my wife (I'm sick of them, but she loves them). The day was kind of a blur, and I sort of rushed through it. Without realizing it until after the fact, I had added all of the extract at the beginning of the boil. The resulting beer was a lot darker (it almost resembled a dunkelweizen), and it had an aftertaste that I'm convinced is what people blame on the extract. The so-called "twang."
Extract does not need to go through a full 60 minute boil. Add a little for your hops at the beginning, but then add most of it towards the end. If you do a partial mash, don't add any extract until late in the boil.