Gremlin in the program?
I've already reported this to web support but thought I'd post it here in case anyone gets confused as I did for a bit:
I was using a companion cert to check fares from SEA to HNL for 12/3 outbound and 12/8 return. Without the cert code the outbound fare for flight 851 on 12/3 was $663.20 for F and $293.20 for Best Deal. Then with the companion cert code the fare box showed $732.05 + $68.85 for F and $293.20 + 68.85 for Best Deal. In other words, the F fare with the companion cert code showed a fare that already included the companion cert (i.e. 663.20 + 68.85 = 732.05) and then also showed the +$68.85 separately. The Best Deal fare didn't do that. It showed the regular fare of $293.20 with the +$68.85 for the ompanion directly beneath.
When you select the flights and go forward the system appears to come up with the correct fare, not charging twice for the companion cert in F. But if you just look at the Available Flights screen matrix it isn't clear that fares aren't being displayed consistently when you have the companion cert code entered. By the way, the Full Flex fare did the same thing that the Best Deal fare did.
I haven't seen this before so I assume it isn't intentional.