If the components which were once on the same line are now on separate lines, there are at least two issues which might contribute to the problem you have. First, the separate lines, due to line length/configuration, might have slightly different ground potentials. Second, one of the lines, probably the one with the pream/CD on it, is connected close to another line in the box which is throwing out some noise.
Kal (not a licensed electrician)
Kal (not a licensed electrician)