Ahoy there, er'body. I really appreciate your help in figuring out what exactly was going on with the phantom proficiency pips the other day. As it's purely a cosmetic issue, I put it out of my mind and continued the game as before without any further problems for the most part. The only other significant oddity that's come up since then is that Minister Lloyd has been strangely absent from his home in the Umar Hills, but unless he still fails to show when I return from the temple ruins and thus interferes with properly concluding the quest, it shouldn't be of any real concern.
There is only one thing at the moment that is really bugging me, and it is a problem not with the game itself per se, but rather the behavior of a particular component of SCS that I installed. Namely, under the current settings, fiends summoned by enemy spellcasters should not be hostile to their summoners. Unfortunately, this is decidedly not the case; if anything, said fiends almost seem to prioritize attacking my opponents over turning their attention to my party. This is frankly spoiling battles against enemy wizards, as I effectively have a very powerful ally in tearing them to pieces more or less for free. It's no fun, honestly.
How risky would it be to try reinstalling this one component with a game still in progress? Obviously, I don't want to screw things up in much more serious ways for the sake of fixing this one issue. I'll not attempt it without knowing what the potential consequences may be. Any advice is appreciated. Thanks, everyone. : D