I was watching them the whole time (I guanoed them so it only took about five minutes for each one). Eventually it worked, so I guess it was just a delayed reaction. Does it have to be the same seeds? I didn't know it mattered.
As far as I can tell it does not have to be the same seeds. The issue seems to be that it only counts harvests after all shucking and planting is complete. Not sure if this is intentional but personally I like that it makes it a bit more difficult to complete.