From the MCF forum thread:

When putting wheat in a craft table it gives back seeds instead of flour and putting Natura's barley in a craft table doesn't give flour. Is this by design? I've looked over the config file and cannot find the one that changes this. Removing Hunger Overhaul enables flour again.

Unsure about how this was handled in 1.6.4.

I can't remember how it was handled in 1.6.4 but what I can say is that I add a (minetweaker) recipe for Barley to barley flour using the mortar and pestle from harvestcraft.
I'm happy getting the seeds from wheat in the crafting grid and then just using either the mortar and pestle or the pulveriser for flour. It would be good to make sure there's still a way for others to get flour, though. Some kind of config option, maybe? Or perhaps it needs a new recipe, eg, 2 wheat in a crafting grid gives (a configurable amount of) flour? Same recipe design for Barley would give barley flour. I'd be very happy with that and I'd be interested to know if others would be too.

The crafting grid flour recipe was removed in 1.6 regardless of Harvestcraft's installation or not. I prefer getting the seeds when putting a single wheat in the crafting grid and would kind of like that for barley, too, but I don't know how the flour recipe should be handled. Maybe a shapeless 2 wheat/barley in the crafting grid making flour with a configuration option for on and off would be a good solution.