Please post a link to the photodiode data sheet or product page.
If the photodiodes are identical, you may have installed photodiodes 2 & 3 backwards. In any case, the voltage divider circuit (shown left in the figure below) will not work well with the Arduino ADC, and when switching ADC channels, you must throw away the first ADC result, and take the second reading.
The circuit on the right will work much better. Use just about any low voltage, rail-to-rail op amp (the LM358 is not rail-to-rail).
Should be OK, if you actually do have the diodes connected the right way around (as drawn). Except that the diode impedance is far too high to be connected directly to the ADC input.
Are you throwing away the first measurement, after switching ADC channels?