I've never worn the shoes anywhere near water. I've always worn socks with the shoes as well (although I did wear them on a particularly warm day in Palm Springs). If it is sweat, how would I go about fixing it? The shoes have been given plenty of time to "dry out", but the discoloration doesn't seem to be getting better. The darkening is also apparent on the inside of the shoe, which rules out some possibilities.
Check out the official shoe care thread. Someone was just talking about the same thing. I don't have the exact link, but they contacted Alden (I think, might have been a retailer who carries Alden) and they were told that it might be oil seeping into the upper, from the water lock sole. Their solution was to "wait it out".