Tested this in my survival- and creative world running the current latest version of AA (r138):

In my Farmer, I've filled every single input slot with a full stack of potatoes. When the first crop is grown, it's harvested and appears in the output slot. The stack of potatoes in the topleft slot of the input side goes from 64 to 63 (as a new potato is planted), and from that moment on no more potatoes make it to the inventory of the Farmer. The Farmer does still break the fully grown crops, but they appear in neither the input- nor the output side. The only thing that occasionally still makes it into the output side are poisoned potatoes.

When I fill up the topleft stack on the input side from 63 back to 64, the very next harvested potato does appear in the output side, but the stack in the input side drops to 63 again and the bug re-appears.

If the first stack of the input side is less than 63, it'll correctly harvest the potatoes and fill up the stack on the input side, but only back up to 63. From there on forward, any potatoes that are harvested disappear.

EDIT: I just tested this with carrots, and the same thing happens. However, industrial hemp for example does not seem to have this issue. Probably because they don't need to be replanted.