Auto-sorter? Like Boss? I already used it for load order. Anyway, obviously I haven't mods that should change the pick functions. This is a mess.
If you want to see if it's mod related, just disable all mod's and try to do mining again !!!!!
The clay can be mined without stop until you have 4000 pieces from it.
The mining spots added by Hearthfire (clay and stone) do not stop at 9 strikes, like the vanilla iron, silver, etc.
So make sure you weren't just trying those two types.
And if you think it's mod related, why not post in the mod forum?
Picking a slightly different place to pick works for me.