Thanks everyone for your feedback!
Neither dog has an ear infection, they do the full body shake as part of their stretching routine. The ears are just loud. I am not sure if they are having any dry skin problems, as i havent noticed an increase in itching, but it is a possibility with the cooler dry air. They both have dog beds in our bedroom, and know that the command "bedtime" means to get into their beds. We have them on a very consistent daily schedule with morning and evening walks, totaling an hour each day (plus playtime/B500 before bedtime).
Last night we decided to carefully b-proof the room, and make sure they were completely settled in. It seemed to do the trick, and they slept great last night outside of our bedroom. Our best guess is that they were over stimulated too close to bedtime the other night, and we just need to be a bit more careful that they have calmed down.