Try the latest version I just uploaded (same link).
Since I am not able to reproduce this error, please start a new project and try to recreate the problem in as few steps as possible. Then, tell me which steps you took to create the error.
I'm actually getting this error with the affixes not showing up in victory aftermath either. I created a new project, loading Yanfly's item core, and victory aftermath, and your affix system. I created a basic affix, giving it a 100% chance to appear on a sword, and setting that sword to drop with 100% chance from an enemy. I go into the game, fight a couple of bats, each of which drops a sword, like so:
But then, when I go into the inventory, I can see the prefix was applied, as such:
Which actually brings me to another problem I'm finding. As you can see in the second image, it's not listing Harold as being equipped with a sword, even though he currently is. If I'm using any item variation via Item Core, then any item that could have an affix defaults to the absolute lowest value it can have with that variance (for example, a sword with 10 ATK at a potential variance of 5 always gets reduced to 5 ATK). Furthermore, if I de-equip it, it gets immediately randomized, as if it's being turned into a completely new item, and the game isn't reading it as one before that. Like in this screenshot, I de-equip the stock sword and suddenly I have three randomized swords instead of two randomized and one plain.
I have no idea what's going on with this. I've tried re-arranging the plugin order with no changes. Independent weapons and armor are active. No messages show up in the debug console to give any clue. Any thoughts?