OK, I ran a test to look closer at starting square resources. I used the same setup as before, and was careful to make sure both were at Noble difficulty. End result: under Civ4, two starts had Horses, two starts had Copper, and one start had Iron (out of five starts). Under Beyond the Sword, two starts had Horses, and one start had Copper. My conclusion: well, first, it's not a statistically sound study, BUT my guess is that there's no significant difference. Anybody who's complaining they "never" get Horses and/or Copper is probably just having an unlucky streak.
There may be one factor, however. Beyond the Sword may be slightly more favorable toward food resources than production resources. I seemed to see more food bonuses in the BtS starts than production bonuses, and vice versa in Civ4 "Vanilla". I can't really quantify it, however. One thing that does appear likely is that the code does take "hidden" resources into account when determining starting positions--in both cases, the starting square had a lot of resources, both visible (Clams Fish etc.) and not yet revealed (Coal Uranium etc.)
One more factor to consider. I believe that the game takes difficulty into account when determining starting position. It's something like the game placing a number of AIs before placing the player, depending on difficulty--on high difficulties, the human is the last player placed. If you're complaining about your start position, it could be related to the fact that you've moved up to a higher level and weren't aware of that factor. And, of course, if you played Civ4 "Vanilla" at Settler but you're now working on Prince, that may partially explain why you're seeing fewer good resources nearby.
Or Firaxis could have secret code that reads your username and gives you a lousy start position if you're someone who does a lot of complaining on the forums.
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