@Magnus - Ignore my instructions. I have the same problem, and was planning to write a post about it. Then I thought I had fixed it yesterday with the solution I described to you, but I think it was just a fluke. (Maybe the windows just happened to be in the order I wanted.)

I've tried Jan's instructions, and they're working for me.

                  (t1) |  t2  |  t3    visible: t1 | t2
 -> Mod+j ->        t1  | (t2) |  t3    visible: t1 | t2
 -> Mod+j ->        t1  |  t2  | (t3)   visible: t1 | t3
 -> Mod+Shift+k ->  t1  | (t3) |  t2    visible: t1 | t3

After that, I can use Mod+m to go to the master window, and Mod+j to go to the "slave" window. Thanks to Jan's diagram, I finally understand what's going on.

Amy