Hello!
Unfortunately, there is no ultimate way for MF Pro to detect whether the previous race is settled other than to check that its bets have been settled. It checks whether you placed any bets in a particular market and if you did, it waits till they arrive in your Account Statement. Otherwise this could potentially lead to situations where BetFair marked the market as "Settled" but the bets have not been settled yet (which happens all the time), so the program "thinks" that it is OK to proceed and follows wrong staking plans etc.
This case is an exception that, I admit, is not processed correctly. However, it happens too rarely to pose a recurring problem with triggered betting.