Here's the problem: prisoners are counted in the census as residents of the place where the prison is located. They can't vote, but they do increase the political representation of the area where the prison is located, and then correspondingly decrease the political representation of the area where the prisoner originally lived.
And this can be significant. With 50,000 or so prisoners in Illinois (I think that figure is about right -- corrections encouraged), that's half a state rep district.
This post here explains some remedies.
UPDATE: I heard from Peter Wagner of Prisoners of the Census. At midyear 2000, the Illinois Department of Corrections held 44,819 people. 60% (about 25,000 people) were from Cook County. They are working on a more detailed analysis of the legislative district impact.
There are no state prisons in Cook County (right?), so that means, at least, we had a quarter-state-rep shift out of Cook County to Downstate. As one of my favorite phrases goes: that ain't right.