Dear Kai,
I am NOT interested in psudo-differential mode. I am
trying to measure 2 single ended channels but the ADC is
not doing its job properly. I am perplexed that why should
there be interefernce from other channel. There is nopossibility
of capacitive coupling as frequency in question is very low.
Then I have checked everything 100 times. I dont see any AC voltage on Ch1 but get it as ch0/8 !!!

There is no problem at present with direct coupling to 4052 as the input impedance of ADC is very high. so not much drop in
voltage. Voltage levels are sufficient for 12bit operation.
The impedance in Ch0 source is 5K6 and that of Ch1 source is
100 ohms. These couldnt be shown in schematic.

The diode in CS line is of old legacy and is now removed.
In other project where this ADC worked well I used just zener
diode for refernce. So due to supply voltage of 5V of uC there
would be current flowing in reference ckt from CS line.(Protection diodes) That would raise the ref voltage and spoil
calibration. So I put the diode in series and it worked. Diode is able to pull adc low for operation. When off the CS line is pulled up by resistor to REF. If diode had made any problem ADC wouldnt function at all.
I think many people would have used MCP3202 in AC signals and hope they post their only configuartion code just to check.
Thanks