So, I finally figured this out. I needed to remove the <FieldRef /> near the end of the CAML query. I'm not even sure why I had that in there anyway. I also re-created the boolean field to have no question mark since I didn't like the way it looked in the code. Thanks again for the help. It's doubtful I would have figured it out without a couple extra eyes on it.
$().SPServices.SPCascadeDropdowns({
relationshipList: "Projects",
relationshipListParentColumn: "Company",
relationshipListChildColumn: "Title",
relationshipListSortColumn: "ID",
parentColumn: "Company",
childColumn: "Project Name",
CAMLQuery: "<Eq><FieldRef Name='Active' /><Value Type='Boolean'>1</Value></Eq>",
debug: true
});
