I forget what I was running but encountered this as well. I wasn't missing boxes, though, I had an additional box which I couldn't add to (it would just create another box). Ended up with 21 boxes, with only 18 usable. Flashed to a different ROM and forgot about it.
This is what I'm refering to...
http://forum.xda-developers.com/showthread.php?t=447972