I bought a 100-load of each reagent. Sometime later I notice that 3 specific ones keep simply disappearing as if they were used en masse. Garlic, Nightshade, and Spider Silk. The only thing I *might* have connected the disappearance with is battle. But it's never obvious when or why it happened. Anybody know the details?

I would guess that while you were buying bulk reagents, some didn't fit into the avatar's pack and a friend grabbed the rest. They only work when the avatar holds them. From there, it's possible a near-death ally can drop items as they flee. This can be stopped by setting their combat AI to berserk so they never run.

The other possibility is they could be stolen. A small number of npcs can pick your pocket. If you notice them hanging uncomfortably close to you and making nonchalant comments about the weather, chances are they've taken something. You can get it back only by killing them, but they can be raised afterward with no lasting consequences.