Differential Op-Amp rising and falling error at zero
Figure 1. A straightened up look at the scope shows the sensitivity settings for each channel.

Your Channel 3 sensitivity is 20 times that of the other channels. It seems to me that the noise is about 1/40 that of the signal.


  How would you compensate for something like this or am I incorrect in thinking its due to differences in response times in each photo-diode?


I'm not sure why you'd compensate. That's the actual error. You've proved it with the signal generator.