I am actually confuse; the timer never stops outside of the dome. you have 10 seconds as soon as you step out of the room and timer won't stop till you either get the flower in which it gives you 20 seconds (there was something behind that idea but not the time to implement it).
Changing rooms happen at the border of the exit/entrance.
When you give back the flower the timer resets to 10.
For room 3 I think i broke the camera with the last update........... I will have to update it sorry for that