Tower of Babel. Being able to get into random encounters mid-jump ruined the jumping mechanics.
I can understand, to an extent. My first time through Babel I had an absolutely miserable time, especially with the last section and the moving Pods. Now it's my favorite dungeon in the game.
But since we're on the topic of puzzles overall, I'd like to make a statement that agrees with you and Kevadu:
Don't put random encounters into your puzzle rooms! I can enjoy puzzles, but when the puzzle requires you to move from one side of the room to the other and you can't even get halfway across the room without fighting it's incredibly annoying. For some puzzles it might even confuse you and you might forget what you were going to do.
Edit: Oh, you edited yours. Yes, there were a few jumping puzzles. The Thames and Shevat had jumping puzzles where you had to jump specifically to get certain items. For example, in the Thames you had to jump on one NPC's head to jump onto a moving crate and whatnot. Kislev also had a few nice "puzzles." They're nothing extraordinary, but they allow you access to extra items and sections.