In confugration B the voltage supplied to the last card is very low so the intensity of the board gradually decrease and does not give nice visualisation effect
later you write
I am already using seperate SMPS for each boards.

This can only indicate that the input voltage to the SMPS get too low.

I feed a lot of LED boards each with their own supply generating 3.3 or 4 volts for the LEDs and 5V for the logic from a 24V line and the supplies I use require 18V minimum. When someone "modifies" our wiring it happens that the 18V is not met and all kinds of "funny things" happen.

If you measure with a voltmeter, you will get a false reading since the PWM regulation or multiplexing of the LEDs will make the load vary at a very high frequency so you need to observe the supply voltage with a scope.

Also do you have large caps (470uF or more) on both sides of the SMPS? that alleviates (to some degree) the pulsed nature of the load.

Erik