If you measure the voltage across the ADC inputs with a multimeter does it show the same voltage as the ADC reading? Try the multimeter on AC as well. You could also try disconnecting your probes from the ADC inputs and connect a 1.5V battery to each input to make sure they are reading the correct voltage.
Is the Raspberry Pi powered from a battery or a switching power supply and are the probes pushed into the earth or soil in a plant pot which is isolated from the earth? If you are using a switching power supply and the probes are pushed into the earth you may have a ground loop between the power supply input and output wires. A ground loop on switching supplies can generate voltages in excess of 70V AC between the earth and the power supply output wires which would cause problems with the ADC readings. It would also explain why the voltage on the ADC input changes as each sample would be at a different part of the AC cycle.
The easiest way to test for a ground loop is to measure the voltage both AC and DC between the probe, when it is pushed into the ground and the Raspberry Pi ground pin. If there is a voltage you will need to isolated the Raspberry Pi power from the earth. The easiest way to do this is to use a linear power supply which contains an isolation transformer.