I had this issue on a trip to Las Vegas a few weeks ago using Northwest PK $$ off certificates to book Continental flights. These types of tickets are booked by calling NW even if you pick all CO flights.

The website will show everything ticketed, but when you go to OLCI, no dice. Call up support, and they say "it's fine, we can't tell you why it's not letting you checkin." That's the answer you get when you're SSSSed.

Turns out the res wasn't under Continental control and looked like a paper ticket. The strange thing was the agent that checked me in never asked for anything. When I got to the PC they looked confused...asked for a paper ticket...did a bunch of typing, and got it set.

Sadly (better for my liver), all of FC had cleared full with EUAs, and because I wasn't officially ticketed it passed me by (only Golds behind on EUA). Made up the drinks and loss at the poker table.

So, beware CO upgrade certs and Northwest PK discount certs for CO reservations. Reminds me I have an EWR-PDX in Feb to fix...