I have always preferred LCD screens, and I like to think that it's because there is something highly resolved to focus on: little square, sharp pixels rather than the mush you see when you look at a CRT close up. But I'm guessing.
I don't know the answer to this, but you could start by looking at the obvious differences between the two:
1. Resolution. Screens can display only about 70-80 dots per inch Paper can display five or more times that.
2. Position. In order to read from a screen you are forced to sit in front of an immovable fifty pound piece of machinery. You are less likely to use different postures than with paper.
3. Light. Paper reflect ambient light. Monitors generate it (i.e. you are reading something which is essentially backlit, more like an overhead slide).
4. Radiation. Monitors generate it, paper doesn't. Can't say what difference this makes.
5. Reflection. Monitors tend to display more reflections than paper (unless it's really high gloss paper). Furthermore these reflections occur on a different plane (the outside of the glass) than the material which you are reading (on the inside of the glass). This quarter-inch difference (more if you have a glare filter) might conceivably have some effect on your eyes focusing...
That's all I can think of. Besides my eyes are starting to hurt...
Also: 6. Flicker. Paper doesn't refresh at 70 cycles per second.
John Gould and his collaborators at IBM did a series of studies on this problem. Most of the reports were published in the journal Human Factors, published by the Human Factors and Ergonomics Society of Santa Monica, California, USA. Their findings were that high-resolution, anti-aliased displays could produce short-term reading performance equivalent to ink on paper. They ruled out age, familiarity with CRT's, and the emissive/ reflective display difference as factors, among others. This summary doesn't do justice to the whole body of work, which I thought was well and carefully done--worth the read.