ADC Reading is much lower than expected
According to your circuit, the 3v supply is connected directly to your ADC - forget about all the transistors and loads - 3V and 0V goes to the ADC. 

Then, according to your measurements, the 3v supply is "much lower voltage than expected". So, you have the ADC telling you the reading is low and the meter telling you the same - what on earth makes you think the voltage is 3v?

I reckon the CR123A battery is "drooping" under load conditions.