Its like a double rainbow, all the way

But seriously. I just noticed in the last hour or so of playing that: Yesterday in game my agility and endurance were in red. Next day, roaming around market selling loot, my strength and willpower are in red, but agility and endurance are in green.

I'm not suffering any diseases or using any magical weapons or anything like that.

I am using a number of mods that might be influencing things (Kuertee's clothing matters; Audacious Magery; etc.).

I always thought Blue = normal; Green = attribute is being buffed (e.g., by a potion or enchantment; Red = attribute is being drained, e.g., by fatigue, disease, enchantment, etc.

Is that not accurate?

I tried running the UOP thing to "Fix Attributes and it adjusted them up by two but they were still red.

You have the right of it. Green means the attribute has been buffed, and red that it is being reduced. My guess is that you are wearing a magic item that is doing it, perhaps both. For example, the Scales of Pitiless Justice buff your Strength, Intelligence, and Agility, but penalizes your Personality.

Either that, or, (iirc) if you get hit by a poison that damages your attribute, that stays like that (and in the red) until you pray at a chapel altar - I think.

Some magical attacks also damage attributes, such as the Will-O-The-Wisp. Aside from praying, you can try buy restore attribute potions. Or just eat the right ingredients. Monkshood restores strength, and primrose restores willpower.

You can also buy Restore spells for each attribute in the various temples around Cyrodiil. Anvil's chapel normally sells 2 of them, Personality and Luck, so if you have the KotN running without any sort of delayer mod then you won't be able to get those. You can create them though if you manage to get into the University.