Daylight doesn't contain equal amounts of all colours. The spectrum of daylight peaks around yellow/green, and the amount of energy falls off quite sharply as you move to the blue end of the spectrum. That means even if the width of the blue filter is the same as a green filter, you'll measure less light coming through the blue filter. If you're using artificial light the effect will be even more pronounced as artificial light generally has a lower colour temperature than sunlight.
Incidentally, the response of your solar cell will also vary with the colour of the light, and this may well also be affecting your results. I can't lay my hands on a typical frequency response for a silicon solar cell, but I think the response falls off at the blue end of the spectrum.