White and translucent clays are more prone to discoloration than the other colors, or maybe it just is more obvious with them! Sometimes they "brown" a little because of the oven, sometimes the clay is just a tiny bit dirty (form hands or whatever) but this doesn't show up until it's baked. I'm not sure, but possibly sanding slightly would remove any top-surface discoloration.
Baking for a long duration (and discoloration) do not undermine the strength or durability of the clay. Not conditioning enough or other factors, like using a toaster oven, CAN. Also, different brands have different strength properties, so Super Sculpey will be brittle no matter how long you bake it but other brands are better.
Some people bury white items in corn starch or something to limit discoloration, since then the powder has to heat evenly for the clay to get to temperature.
So, lots of factors can be involved. But if you plan to paint this one, probably it will be fine.