I have just tested this several different ways, with and without a backpack and I did not experience this problem. I have noticed at times Inventory Tweaks may make items invisible and hitting R to resort them will make items appear again.
Anyone else experience this?
I tried that and a few other things, sometimes opening a different inventory works, but not this time. Re logging didn't help either.
Got some more seeds between posts and random crops are disappearing when I harvest. Most of the time I do get the produce, but the plant is gone and no seed drops. This is both with traditional harvest and the right click with empty hand.