The number of waves is the green number on the right side of the screen - NOT the number that is popping up in the middle of the screen after each wave. If you want a level 40ish rift, you should set the number of waves at 9 or 10, most likely.
Not sure if this has been asked anywhere, but is there a way to have the bot clear the entire rift even after the boss has been killed?
Edit - also, this profile works incredibly well on my barb. Thanks for all of the hard work.
For people having a problem where the bot stops after running one rift, make sure that you have NOT renamed the file and that it doesn't have a number on the end of it because there are multiple copies of the file in the directory.
The file has to be named R-RIFT.xml and nothing else.