I checked the markers in the CS too, and they do seem correct...
To be sure I went to Jerall View, and I confirm the sun is raising in the north in my game.
I've also checked in tes4edit, and only UOP and OOO add north markers and the one in Jerall View is not modified.
Now at level 30 I started the main quest, everytime I come close to a oblivion gate the sky become red and it start storming and raining! and this special weather is prolonged for several hundred of feets; now if i enter an interior (house, cave, ...) and go out or open a letter/book in my inventory and close it, the weather become normal (no rain, no storm, no red sky)!
As I was already doing some "sun check" I also did some oblivion gate checks. ^^
I tried to open a book during an OB weather (within and outside the gate range) and I wasn't able to reproduce what you describe. Is there something else to do?
Concerning the change of weather when entering and exiting an interior, I believe it's something that cannot be modified. It's linked to the weather transition that cannot be tracked between a change of worlspace or exterior/interior. So if the weather is in transition, you'll have either the previous or the target weather after entering and exiting an interior.