I can confirm this bug still exists in 1.71. Thanks for reporting it; now I know I don't need to hunt through forge items.
Observed effected entities:
Fertilizer (bonemeal + scrap)
Stakes (er 4 sticks; forget the name offhand)
I also noticed inconsistency between client/server stacks (the client would stack but the server would say no).
From the description and observed behavior: I -think- the issue is opening the crop-analyzer shows the hotbar, and thus this code tags /all/ items with an empty NBT array, irrespective of the item type.
A test for confirming this with known clean parts (or dirty parts to see if they all become dirty); would be to place test items in the hotbar, open the scanner (might require a scan operation on an unknown seed sack) and see if the problem is reproducible.