I can't provide any references to support this but I have heard fluorescent lighting is hard on the eyes. I think is had to do with a flickering of the bulbs that is not really perceptible to you but your eyes pick up on it and react to it by constantly trying to compensate. Thus the fatigue you're experiencing. I get the same type of eye fatigue under fluorescents, but no headaches.

As for a solution? You might try using one of those small battery powered clip-on book lights for reading at the library and classes. If you're at work in an office try setting up a halogen or incandescent lamp to overpower the fluorescents where you're working.

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