Why would only the top outlets work in my two kitchen receptacles?
Usually, a red and black wire connected to an outlet with a broken off tab indicates that one of the outlets is controlled by a wall switch somewhere. Typically this is used to control a light from the switch next to the door to the room. However, this is an unusual configuration for a counter-top outlet in the kitchen since usually the lighting is ceiling or cabinet mounted.

My next step would be to try to identify a wall switch that could be controlling these outlets.

Alternatively, just disconnect the dead wire, cap and tape it, and bridge the screws on the hot side of the outlet.