The call centre operators just repeat the mantra "it's because we invoice monthly in arrears" and cannot explain any further. I guess it's not in the script and they are just underpaid droids. At least the phone works, even if they can't add. Such is life in Africa.
Update 22nd June 2011: After meeting with several MTN executives they helpfully sent me a reconciliation spreadsheet going back several years. I then discovered the following:
I am therefore left with the conclusion that all statements between Feb 2009 and Nov 2010 were incorrect, and the bug has now been fixed. Weird.