No, that's quite normal, what you are seeing is your input frequency being chopped up by the reference clock, the result is the numbers jump according to the ratio of the frequencies. However, 2KHz is far too high for the clock, remember you are trying (at least for now) to generate a gate period of one second and as it will be a square wave from the flip-flop, it needs to be at 0.5Hz (one second gate on, one second gate off). As you are dividing by 4 in the CD4013, your 2000Hz should be 2Hz.
There is a final stage to the project, that is to sequence the gate, latch and reset signals correctly. You need to reset the counters, gate 1 seconds worth of input frequency to the counters then latch their contents to the display.
Brian.