Timmer command is actally after the TRIGGER starts, not the Scen. So if you turn the trigger off to begin with (You do know how to do that, right?) and then activate it with your first instruction trigger, and have the second one with a 5 second timer (or whatever) it will work in my experience.
As for your 'Blue Hill' and 'Guy walking on Water' question, I assume it's bridges that have been placed in the Map Editor, then removed with triggers in game.
See, they create a patch of 'Walkable Water' in game. Note. It's only the middle parts of the bridges that do this.