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!"^[1]

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.^[2]

Note: The Gray Race and Stranger Than Fiction are tuned at A440.

References