Whenever I seal an experimental affix with a Rune of Research it consumes 2 runes.
https://imgur.com/a/0y8SDYq
Edit: Seems to be partially a visual bug. Using a different rune after using a rune of research seems to set the counter correct again. Will have to test with using runes of research in succession.
Edit 2: Changed title - On using a rune of shattering the count went down by 2 yet again, on using another one it goes down by 1 again.
My findings:
It seems to have to do with the crafting material stash total count.
When selecting a rune in the Forge it removes one from the crafting inventory but the count shown in the forge is still the total amount (crafting inverntory + the one in the forge).
When then used it automatically places a new one in the forge. However the count in the Forge then shows only the amount of runes in the crafting inventory and doesn’t take into account the (new) one placed in the forged anymore, thus making it seem like 2 runes have been consumed.
Having the crafting inventory and Forge open at the same time and r-clicking on a rune 3 times also makes the count in the Forge mess up an make it seem like you have 1 rune additional.
On first click it removes 1 from the crafting inventory and places it in the Forge.
On the second click the count in the crafting inventory goes back up again by 1 but the Forge count stays the same.
On the third click the Forge count goes up by 1 again, and the crafting inventory stays the same.
https://imgur.com/a/QXnVU8y