When there's a problem with BetFair API, it doesn't matter whether you are logged in to MF Pro or not: the program asks their server for your current funds and list of bets every several seconds, so if the API is down, you'll notice it immediately as it won't be able to proceed.
I'm really sorry to hear about this annoying stuff, but there's little we can do.
Update: right now their service is unavailable again. It returns an error message when trying to connect.