The real reason for it was because the South, as usual, wanted to have their cake and eat it too.
Until the end of the Civil War, the Southern states carefully stipulated into law that slaves were "property," thus things like the Fugitive Act, the Dred Scott decision etc. But of course they wanted the property to be people if it ensured them more seats in the House.
One of the first articles of the Confederate Constitution reaffirmed slaves as property.