The redstone particles around the open crate mean that any items it drops have a significant pickup delay for flowers. How long did you wait? Also, can you check (with the Wand of the Forest) that you didn't accidentally activated state-sensitive match mode, and something in the pack causes the "example dirt" 2 blocks below the flower to be different from the target dirt it's supposed to place on.
You might also want to compare (via F3 debug screen) that those two blocks are indeed just dirt blocks.
