Teo,
Your OPA381 output is clearly driven to its positve rail: (V+)-500mV. Does your simulation shows 2.8V output voltage or do you measure it in an actual application?
If you simulate the circuit, do you run DC sweep or transient analysis; if you use transient analysis, please make sure your I2 photodiode current of 9nA, does not change with time. I have simulated your simplified circuit and obtained expected result (Vout=~347mV); please see below and attached Tina-TI schematic.
If you built the circuit, what kind of PCB do you use? Is it possible that it has significant current leakages? Also, please check the output with a scope for any sign of instability.
