The system goes by a moving average of your posts, through several time lenses. I can't give more specific information about how the algorithm(s) at play there work, except to say that zeros count like they would in any other average.
If you have 5 posts to your credit, 2 of them negatively scored, one positively scored and two zero-scored, the zero scored posts only hurt in that they extend the breadth of the average, thus lowering your average score just a bit.
The goal of the question limiting system is to slow folks that dive in without really understanding what's on topic a bit and give them more opportunity to look around and get to know what the community reacts well to seeing. While your migrated question wasn't bad, it was migrated because it wasn't on topic - hence, we still need to count them. As others noted, migrated and deleted questions do stay in your history, and the system does look at them.
If you have only positively or zero-scored questions, then the zero-scores won't immediately cause you to see the limits kick in, but a single down-vote with so many zeros in the average probably would - and that's how it should be. If you have more than a hand full of questions, at least a few out of every 10 should have an up-vote or more.
But, you were only limited for a very short time, it got your attention and made you wonder how you wandered into such a thing. That's precisely what it was designed to do - please don't be discouraged. You had just enough in your history for it to find you in scope.
One or two more up-voted questions should ensure that you never see it again. It's there to help new users not have the horrible experience of trying 15 questions in 3 days and ending up with a much longer (and harsher) block, something we were seeing quite a bit of on larger sites.
Just to note - edits made to your own posts and up-votes you receive from answers you write on other questions help boost the overall indicator the system examines. All it wants is some sense that you're being careful and trying to contribute quality, and it'll (in most cases) simply get out of your way.