I was recently hit by a glitch in the system. Booked low fare on CO.com and was shown the (correct) 100% EQM. When I flew, I was upgraded to FC at the airport. My account was credited only 50% for that segment. When I called the OPSC the agent told me that it must have been the fault of the gate agent (making an incorrect entry not showing how I purchased the ticket). He had no way of verifying that I purchased the ticket at CO.com, but took my word for it and gave me the full 100%.

Jack