In full disclosure I figured out what I did wrong - what an idiot I am.
Yes, it was a case of using the $25 certificate on 2 tickets...that's it! So it divided it up between the two, $14 should have been $28 (not sure how that worked, but I think someone else mentioned they also got more).
I just used it for one ticket that was $99 (including tax) and it brought it down to $72 (including tax), so a savings of $27 (don't know why, but not complaining).
Then I used the other one for the other person.
Since we have so many miles stockpiled, if it happened again (late luggage) I would again take the cash - less cash out of my pocket, the better I like it.
But I have a question...if the fare should go down, can I claim the Best Price Guarantee? I mean, does the fare have to go below $72, or just below $99?