Just a shot in the dark here, but when I see something like this happen in my games, it's usually because my satellite is running out of Electric Charge. All SCAN sat devices require a constant supply of EC or else they stop scanning. Your vessel goes behind the celestial body, batteries keep it alive for awhile, it dies, then it clears the planet and you get sun (and EC) back. If you keep an eye on the resource panel through a complete orbit that should tell you if that's the problem or not. If it is, you either need a vessel with more batteries (or a way to produce power that doesn't require the sun) or you can wait for the planet to rotate such that those areas eventually end up on the day side as you pass over them. Depending on how well your orbit and the planet's rotation are in sync, this may require you to wait as the planet revolves around the Sun...
If that's not the issue, then... nevermind this post.