Settlement production in 1.4 uses a buffer system, each structure tries to keep a buffer of input resources, and of output resources. Settlements will queue production as needed to keep those buffers. If that over 300 turns (if memory serves) of production has been queued, but it isn't enough, then an "insufficient resources" warning will be given.
So even if you have a lot of food in the settlement, there might not be a high enough rate of production to avoid that warning. Do you have a lot of barracks? They can be food hogs when a lot of soldiers are housed inside.