Changing the document size in Illustrator via File > Document Setup does not update the rulers to accommodate the new document size. Consequently, all your positions will be off in the Transform and Control palettes.
Fortunately, it’s an easy fix: If your rulers are hidden, show them with CMD+R (CTRL+R), and then double-click the vertex, or intersection, of the two rulers. That double-click will automatically make the rulers snap to the document origin–the bottom-left corner.