I just put up an update on the Asset Store. There were 3 discrepancies with the upgrade. LookAtTarget script (fixed by making its GUID match NGUI's), Orc prefab's GUID matching NGUI (which it shouldn't have been), and orc armor material's GUID matching NGUI (also shouldn't have been). I fixed the first two issues, and left the last one in there on purpose. Now when the upgrade is successful, the orc's armor will turn white instead of its original red (just to make it obvious that you've changed something by upgrading).
That said, the upgrade process works fine. If you grab the update and it still happens for you, then you are not deleting the DLL that comes with the distribution version of NGUI (packaged with the HUD Text). Make sure you are deleting the NGUI folder from a new scene. Nothing should remain. After you delete it, you should see 3 errors show up in the console log that will remain there until you import NGUI again from another package (full one).