Video showcasing the issue

When I first installed the mod it worked as intended, however now this is just what happens all the time, the recipes are pulled from the storage however they are placed in the wrong order, also when I try to shift click on a recipe it pulls the first item only, so for example if I shift right click a stone pickaxe it will try to fill the first slot with 64 then carry over to the next, if I don't have 64*3 cobblestone it will just stop the recipe there and not try to balance it