If I go into a passageway and go back up the end I came down, I end up in the room where I didn't come from.
So going down one way, and going back up the same way takes you to the other place instead of the place you went down.
Passages broken?
You didn't mention the version but in 443 passages are working perfectly for me, entering and exiting either side.
Please post the broken quest.
Uhm, I figured it out. although its still a big in my book...
Walk to the left or the right of the entrance point(make sure the left or right is non-solid), then go back up.
ah, so you have stairs wider then 1 block in the passage?
Current passage behavior is to send Link to the destination if he leaves the passage room from anywhere but the tile he entered on.
Since this behavior is reasonable, and changing it might break old quests, I'm inclined to declare it Not a Bug.