That is your problem with the splotchy look on your siding. When the temprature gets that low at night you get either frost or dew on the siding and it will flatten it out. It will be flatter between the studs and from the pictures that that is what you have. If you are going to paint this time of the year you will need to stop at 2 or 2:30 in the afternoon to allow the paint to dry enough not to be affected by the dew and or frost and you may not be able to start until 10AM to allow the siding to warm up.
It is not a problem with the siding or the paint but you will need to apply two coats on this siding if you use anything other than a flat finish.