I know I could probably try trawling the online archives of the magazine, but this came to me while traveling and largely limited to my phone. This was a short story in an issue of Dragon magazine, probably in the mid-90s. I don't remember a ton of details except that it felt like a Western and there was a cinnabar mine driving the conflict. There was magic and also flying airships and pistols, the latter two powered by the cinnabar, I think.
This was from the long-running series, "The Voyage of the Princess Ark", set in the Red Steel/Savage Coast setting of Mystara. Cinnabar magic came up in part 19, contained in issue 172.