I'm not hopeful that anyone will see this, given the level of activity here, but I don't know of any other place that is likely to have the answer to my problem.
Basically, the Virtue mod has started penalizing my Virtue every time I kill a non-evil creature, even if that creature is not an Innocent. I first noticed this when I was exploring the sewers and killed a Carrion Crawler, which dropped my Virtue by 2. Then it happened again with a trio of Huge Spiders, and again with some Mutated Gibberlings, and again with Theshal (the zombie "mayor" that you encounter in the Unseeing Eye quest) and his followers. In each case, the problematic creatures seem to have been of neutral or good alignments (none of them were Innocents). Before long my alignment had changed from Chaotic Good to Chaotic Neutral, and good-aligned party members were either leaving or mad at me. This is especially annoying because I'm certain that there are quite a few more non-evil creatures that I will be required to fight in the course of the game.
I've used Near Infinity to change the alignments of some creatures to evil, which seems to solve the problem, and after some experimenting I found that I can alter the Global "D0Change" via the console to offset the penalties to Virtue and party-member-happiness, but obviously this is a less-than-ideal solution. If anyone has any idea as to what might be at the root of this problem, please let me know. I really like the idea behind this mod, but these persistent bugs are irritating.