[...] when a particular pair is over white surface the voltage at the connector is around 0.4V while that in the case of black surface it is about 3.5V.
If that goes for each pair when unconnected and change to only responding to the D11/D12 pair when connected, the problem is clearly not in the part that the schematic covers.
Did you try swapping that pair with another to see if the problem follows this pair or stays at the same connector pin?
What else did you try to isolate the problem?
Connector is connected to ADC of ATmega128.
Each to its own A/D-C input pin or...?
I've checked the output of each pair on LCD. No output pin is shorted(I checked it using a multimeter). Still the readings on the LCD show a change only when the pair connected to 8th pin of the connector experiences a color change. My ADC settings are:
Why use A/D-C at all, it's slower and takes more code than using comparators.
Is that your update speed or..?
Readings for black surface: Around 1000;
Readings for white surface: Around 100;
Sounds like it work, just choose 316 as the above/below value.