For example:
Worktable.addRecipeShaped("carpenter", <quark:vertical_planks> * 3, <ore:carpenters_hammer>, 3, false, [[<minecraft:planks>], [<minecraft:planks>], [<minecraft:planks>]]);
must be a "vertical", but it is "horizontal"

What version of the mod are you using?

1.4.8
my bad

I'm using 1.5.9 and seems to work fine.

JEI:

Crafting:

I just fixed a bug with JEI recipes displaying shaped recipes as shapeless about an hour ago in issue #12.

This might be the issue you're experiencing.