I may have stumbled on a rather obscure issue with the Rune Crafting Altar. Essentially, when you put the materials in and then shift+click the rune to "craft all", the "Times Crafted" vanilla statistic does not increase. It works properly if you manually click out the stacks one-by-one, and it works if you are using the "craft all" function to make runes in a vanilla crafting table.

This only really matters when using other mods that rely on those statistics (like Pufferfish's Skills), but thought I'd mention it.