Since it occurred again and was driving me mad - I spent even more time investigating the issue. Here was the problem...

In the screen I've attached, you can see I've highlighted 4 layers. These are four separate layers. The rain in my game/animation has maybe ~40 layers within a graphic, each a rain drop. When I had 4 instances of these graphics on one layer - Animate would shit itself when trying to export... for some reason. When I put each of the 4 instances into their own layers, as per the screenshot, I am able to export a video/SWF properly.
One layer + 4 graphics (each with 40 layers inside) = export stall. Four layers each with a graphic each = export success.
I ran the test many, many times and it happens only when I put them all back into a single layer.
Hopefully that helps someone else experiencing the same issue some day. I just wish I knew why it occurred.