Alright @chrisandeden, this mystery actually taught me something about flex I did not previously know, so hats off to you, because that doesn't happen very often.
There are a couple moving parts in action here. On Tuesday night/early Wednesday morning, there was a change in your forecast for the next couple of days. This change indicated that your zones were not going to be able to make it until your next scheduled watering day without dropping below their allowed depletion line. This was when the decision was made to run Wednesday.
However, your system also recognized that your zones still had a relatively high moisture level. Rather than run the normal duration, flex will only run enough to top your "bucket" off. So those one minute runs were just topping your moisture levels off to make sure that you could make it to the next watering on Sunday. I don't know about you, but I feel like this is pretty damn smart. Some next level smarts.
I do understand that it never feels right to water after it rains, but with your restrictions, it was looking like you would be dried out by Sunday, so flex had to compensate. If you think you zones would've been fine, let me know, because we may be able to tune your zone settings in a little more to solve for that.