9th inning, Sparky sends in a pinch-hitter for the pitcher.  Other Sparky brings in a new pitcher.  My Sparky pinch-hits for the pinch-hitter: the new batter promptly drives in two and I end up winning the game - so there are NO complaints here.  You see this multiple-substitution thing happen all the time both in the Sim and in RL.

The kicker is, this was in a clone league, and the second pinch-hitter was a clone of the first one!  No lefty-righty advantage, and I assume the Sim doesn't track matchup history and adjust accordingly (it would be cool if it did, though).  Any thoughts on Sparky's logic here?

Give a game (box score) link please.

It almost definitely has to do with your pinch-hit hierarchies vs. L and vs. R.  I don't know if you set your own, and if not I don't know why the auto settings would have that hierarchy change for two clones against opposite hands since the situation "ie. need power/need contact" hadn't changed.  But I'll bet if you look at those hierarchies you'll see that that's what happened.

The one thought that I do have is that walks may be determined before handedness corrections are factored in.  I don't really remember.  If that's the case then it would make sense that the version that walks more might get a bump against the opposite-handed pitcher.

http://whatifsports.com/slb/Boxscore.aspx?gid=15774490&pid=1&pbp=0&tf=10

I haven't had a chance to look at your suggestions yet (long day).  In response to the hierarchies, I don't generally set my own for teams like this - no special abilities on the bench, everything maxed out for the eight starters.

Edit - I checked a couple things.  First, the pitcher replacement was righty for righty, so the first pitcher probably hit his pitch count.  Second, in every PH hierarchy the Beauchamp who came in first (and was subsequently pinch-hit for) is listed before the one who pinch-hit for him.