This also happens if your ticket has been changed for certain reasons. If I call for a voucher due to a price decrease, Web Checkin won't work because my ticket number will have changed. Once when I called web support because the online discount hadn't been applied, they fixed my ticket and refunded the difference -- and as a result, Web Checkin wouldn't work.

I called web support about this, and they said it's a known problem. They said they were working on higher priority items at the time, like online seat selection, and that the kiosks would still work (which they did.) They also offered to credit my MP account for the 500 mile Web Checkin bonus, which I appreciated.