[Solved] Transimpedance Op-amp decreasing small signals amplifying larger ones?

Read the notes starting from page 6, it gives you a lot of background information. I was wrong in my assumption that photodiodes and phototransistors work alike.

APPLICATION SCHEMATICS FOR PHOTODIODE-BASED AMBIENT LIGHT SENSORS
A sensitive, FET-input type of photodiode preamplifier, with a very low input noise, should be used, such as:
• Linear Technology LTC6240
• Texas Instruments (OPA827)
• Burr-Brown (OPA128)
• Analog Devices (AD549)