If it's what I'm thinking of, it's the reproduction source material.
Since the Titan books were able to use the original artwork for the reprints, there's very little, if any, change from the original floppies to the TPB form.
I'm guessing (so don't take it as gospel) that IDW isn't able to use the original artwork and have to go about it in the same manner that they're reprinting the Classic G.I. Joe stuff (from vols. 6 and up), which is why some things look different in the newer trade.
I know when I color stuff B&W artwork in Photoshop, I use a top layer that is multiplied that will thicken the lines a bit. Maybe this is what was done?