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The band started playing whole shows tuned a half-step down sometime around 1995. Jay: "We fooled around with alt tuning for recording a bit, but that pretty much sucked (except for Infected!). The reason is, it is much easier on the throat to sing a half step down, so it was either sacrifice a bit of guitar tone, or lose more songs off the setlist... and possibly have to shorten out tours even more!"
The reason why they don't also do this on the records, is because Greg Graffins' voice always sounds better at the top of his range. So for a recording, it's best to get him in his "best" register, as he'll only have to sing it a couple of times and they're done. Singing like this night after night is just not an option anymore.
Another reason is that guitars always sound better tuned to A440.
Note: The Gray Race and Stranger Than Fiction are tuned at A440.