I saw a closed issue on this already and it fixed AgriCraft compatibility.

But I am on mod version 1.7.10-1.9.11 with the latest Forge as well. I do have quite a bit of mods, but even vanilla crops are eaten?

I have the entire set up correct, but any crop that crows instantly gets deleted even with different chests. Not sure what's going on.

Did you tried with vanilla chests?