I've not tried riding in boots since college, but my experience in doing a lot of running in boots tells me to pay attention to how you have them laced (assuming they're lace ups). Make sure you have no impairment of mobility to flex/extend through the regular pedaling motion. Sometimes it means using an alternate lacing pattern to de-stress the area over the ankle to allow more mobility (without impairing lateral support).

I rode through an ankle sprain in college by wrapping it, but it wasn't winter :-)