Phototransistor responsivity does not match datasheet?
The two LEDs are specified to emit the same luminous intensity, measured in candela. Luminous intensity is normalized to the human eye response, so that a red LED and a green LED emitting the same luminous intensity (10 mcd, in your case) will appear to be equally bright when seen by the human eye.

The responsivity of the photodetector, on the other hand is specified in terms of irradiance (mW / cm2). There is no correction for the human eye response, and indeed your device is sensitive well into the infrared, where there is practically no response in the human eye.

The Wikipedia article Luminous Efficiency gives a curve that shows the standard assumptions about human eye response that relate these two ways of measuring brightness. 



Given the two wavelengths involved (565 and 635 nm) it looks like the luminosity difference between these two wavelengths is pretty close to 2:1, which means your red LED must produce close to twice as much optical power to have the same perceived brightness as the green LED. 

This accounts for a large part of the 2.5x difference you are seeing in the  response to the two LEDs. Another factor of 1.2x or so can be attributed to the difference in spectral sensitivy shown in the phototransistor's datasheet. 2x times 1.2x is 2.4x, so that's pretty close to explaining an overall 2.5x response difference.