Two circuits grounds do not match!

I have two digital FPGA design boards which use digital ground all perfectly designed 4 layer PCB(2 layers for double side ground). These two boards have two major FPGA chip soldered along with some leds and switches. Now the case is that I use to send data(sda) from one to another using one data bus and one clock line(sclk).Along with this a ground and a ready signal is provided(4 wires). Problem here is that the leds in the receiver board flickers when I connect as usually.This should not occur,coz that is not how it's programmed.IC is programed to display received data from sda.When I provided one more 2nd wire for ground, this problem is solved,program works as expected.I get data displayed in led.No flicker.so 2 ground wires are required to solve the case. I use 5V Dc supply seperatly for these 2 boards. When I use same source this prob doesn't happen.Why isn't the ground shorting with one single wire? perfectly when different sources are used. I tried using big wire,fat wire,shielded cable and also measured the resistance between the two boards ground after shorting with 1 wire but it's almost zero.Noise level is under normal level.Please suggest me if there is any way that I can overcome this.It appears so strange and crazy in electronics!.I guess it's not ringing/looping since it's purely digital ground with isolation. My freq is 200KHz.Thanks