I experienced a annoying thing on the same place. I saved my game and when restarting I found my little heroin at the surface of the room half filled with water, just below where you have to jump up the tube and into the room with the clockworks. Everything else works fine, shortcuts and all, but aren't you supposed to continue the game on exactly the same spot where you left it (=the upper red crystal in the sun temple)?
Really annoying since the climb is quite difficult.
That actually just happened to me as well. I jumped up to the red crystal without raising the water level and thus saved outside of the water, maybe that caused the problem for me. I can send you the savegame if you like.
