this is more of a work-around then an actual fix, but if you'd like the animation to be slower, you can duplicate the frames in the auto-tile image file and put them side by side. for example, the frames would go 1->1->2->2->3->3 and so on. theres no limit to how many frames you can have for an auto-tile so go wild!
unfortunately as widderune said theres no easy built-in way to make auto-tiles faster, and the method above cuts the framerate in half. there may be a downloadable common event for this on the developer's website, but you'd need some japanese language ability or a lot of dedication to copy/paste text inbetween a translator.
good luck!
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