I think that by using Lahman, there's a bit of a statistical boomerang effect going on. I may not be able to verbalize it too well, but what the heck.
If the game is basing its defensive ratings off of TC or RF, then infielders on teams with multiple strikeout pitchers or flyball pitchers are going to suffer some damage to their defensive ratings because they won't be getting as many chances as they might with the Roy Halladay (shameless plug) types who keep the ball in play and mostly on the ground. Thus, the real life (insert team name here) pitching staff's tendencies and makeup has effected the defensive ratings for the imported players on said team, which may or may not be importing that pitching staff optimally putting said team into a potential heap of trouble. Now a pitcher who puts the ball in play often, say...Carl Morton from your 1974 Braves goes out there to pitch with a defense behind him that is less effective than it was in real life, he's gonna be in trouble. I can't explain Phil Niekro, except to echo the sentiment above that maybe the game doesn't deal with knuckleballers too well.
As for Belanger, arrrgh! Why can't the AI recognize that his defense is what that pitching staff needs. Although some of those Oriole staffs were a bit fly ballish according to Baseball-Reference, which might dampen his defensive excellence depending on what year he is imported in. I don't know how difficult it is to code, but for the up the middle positions the AI should be taking a defense first position because that's where a lot of the action is. Frustrating eh?
My only suggestion would be to get a database that uses neutralized stats like the Spritze DB 2008, especially if it has the fielding adjustments for the problem I've been talking about (not sure, but I do know that the original Spritze/Garlon or Garlon/Spritze DB worked on this very problem and I did stay at a Holiday Inn Express last night

) as well as a whole bunch of other cool sounding features. I can't personally vouch for it as I have yet to use it but it sounds like it might help fill in some of the defensive gap that Lahman can't begin to deal with, as well as CS in the early days and a host of other issues that Lahman (despite its brilliance) has come up short on. Could in fact be a database issue as opposed to a game engine issue...whatever it is, hopefully the geniuses around here can figure it out so this game can hit the warp speed button.
EDIT: Just realized that Spritze DB 2008 is not neutralized, while Garlon/Spritze or Spritze/Garlon is. Sorry for the confusion and maybe Mr. Spritze or Mr. Garlon can edu-meh-cate me and perhaps others as to the differences between the two.