It looks like the rooms where you can't rotate happened because, as you can see from the outside, they are flat. Or as flat as they can be in 3D space

The reason the question mark "fades out" because it is for the room behind the room you are looking at.

I always found the game amazing because it's rich lore made so much sense and I loved the way that it was delivered with hardly a word. I'm now realizing that as a design it is objectively not good at communicating the lore, it just so happens that my brain apparently speaks the same abstract language that its developer did. That's worrisome, considering I am making my own games in turn lol.

1:00 Congratulations, you found one of the worst puzzle rooms in the game! It's a worthless puzzle! If you figure this one out, you're definitely too big brained for Fez. 18:46 Wow, way to not door. 0: 15:14 Yer' countin' wrong, kid! You've completely malformed the entire counting system. 20:40 You finally got it! Now go solve the others! *You can't solve the weird cairns/marker stones yet.* 25:12 Another puzzle you can't solve yet! 29:55 You found it! It's worthless, because the game's visual design language is about as subtle as a brick wrapped in a slice of lemon.

I think most of the problem you're having with the map is that you can use LT and RT to spin it, so you can see it in different perspectives

Ahaha, this one was quite funny. Three equals eight. Reading the story on the wall backwards. Interpreting openings in a skull as additional eyes and... well, the "smiley" I suppose is quite accurate (it being the bones of jaws) but totally looking at it backwards.

SZSZSZSS. There are tetrominoes on the wall in the throne room at 12:33, which can only be seen during rotation. The throne hides them.

I spotted something you didn't in the throne room :O

I love Fez but some of the puzzles ARE bogus, like that first room you were in.