It looks like your black food coloring is changing color. Some colors and brands are less stable than others. That's why they market no-fade purples and reds, as these two colors are especially prone to fading and changing. Though I can't say that I've seen any non-fade blacks on the market, but I haven't looked. What brand of edible ink cartridge are you using?
I doubt it's the substrate or the corn syrup causing the trouble, as I've used edible papers on both royal icing and fondant, and always use corn syrup to apply them, with no trouble. But I am usually using stamped or pre-printed papers (that I did not print myself).