Yes I've found some very strange things (again)

1. Why can't you use Imoen's portrait when you're creating a character (does this suggest that Imoen plays a bigger role than any ohter character in the game)?

2. Jaheira loses here shapeshifting abilities for a while in the game, but when I looked later they were there again.

3. In the manual it says that assasins must be chaotic neutral or evil, but when you make an assisin it can be any alignment exept from lawfull good.

Do these things seem strange to you (again)

The Jaheira losing her skills thing is probably a bug.

The Assasin thing is probably a misprint (it also bards can climb walls and detect illusion)

The Imoen thing is most likely because she plays an essential role in the game and it would not be right to let the main character look like Imoen.
I think it makes sure that you enjoy the story more.