NPC Weapon Proficiencies Not Working. Any ideas or solutions?

Hey everybody. I've run into a rather odd problem and I'm not sure how to handle/fix it. I've been using EE Keeper to modify various creatures, fixing errors, and updating creature files for a mod that I've been working on for a bit. However, I can't seem to give creatures their appropriate weapon proficiencies.

For example, if I take a creature and add two ranks into longswords, no proficiencies show up in the game (viewed with the debug CTRL+Q) and the creature is obtaining no benefits from those proficiencies. This is true for both PC-classed characters (such as human fighters) and monster class characters (such as hobgoblins). They're definitely picking up the penalties for lacking the proficiencies (in my 2da settings, 0 points in a proficiency gives a -1 to hit and -2 to damage) which they're receiving correctly. Just I can't get proficiencies on them, and I'm not sure why.

It doesn't seem to be an EE Keeper issue as when I add proficiencies to party-NPCs, it seems to work A-OK. When I save and reload a creature, EE Keeper shows the correct proficiencies. This is causing a big problem for my mod, and I'm at a loss. Any ideas folks?