I just had to wait 24 hours for a LH flight to clear after purchasing on CO.com. As I understand it the reason for the wait is that CO. does not have access to see if the seats are available at the price they are quoting. So you purchase the seats, they put in a request to the other airline and then the other airline checks things out. Because I was changing a previously canceled ticket to begin with I had to call CO.com to do get the ticket. When I called at the 24 hour mark, they said that LH actually said to give them another hour. So I had to call back an hour later. Then it was purchased.
When you called did you call CO.com technical support or just the regular customer service line? The CO.com people I talked to (and I talked to three, the first call to change the ticket, the second 24 hours later, the third 25 hours later) and all three had no trouble understanding what was going on as they probably deal with this more than the regular agents.
One thing that is odd though is that the new reservation still shows up under the inactive reservations tab on CO.com. But I have received the email receipt, so I know that it has been purchased. But I will probably had to call CO.com a fourth time to get that changed, just don't feel like doing that now.