If you are saying that your finished crust bakes up with a blotchy appearance, you might want to look for drying of the dough, crusted dough will not color very well diring baking. Be sure to wipe your dough balls with oil after putting them in the box to help prevent this.
The use of excessive amounts of mineral oil, like when using a divider and or rounder can also create the same type of appearance. If none of this looks familiar, you will need to give me more imnformation to go on.
Tom Lehmann/The Dough Doctor